Systemic genotoxicity as blood marker for allergic inflammation

ABSTRACT

The invention provides a method for detection of allergic inflammation in a subject that comprises assaying a test sample of peripheral blood from the subject for a marker of DNA damage. An elevated amount of marker present in the test sample compared to control sample is indicative of inflammation. The method can be adapted for quantitatively monitoring the efficacy of treatment of allergic inflammation in a subject. Markers of DNA damage include single- and/or double-stranded breaks in leukocytes, oxidative DNA damage in leukocytes, or a marker of nitric oxide oxidative activity (protein nitrosylation in leukocytes). This unexpected discovery of markers of systemic genotoxicity present in circulating leukocytes enables detection of allergic inflammation with a relatively simple and minimally invasive assay using peripheral blood.

This application claims the benefit of U.S. provisional patentapplication No. 61/861,380, filed Aug. 1, 2013. This application makesreference to U.S. patent application Ser. No. 13/865,798, filed Apr. 18,2013, which application is a continuation of U.S. patent applicationSer. No. 12/761,330, filed Apr. 15, 2010, which application claims thebenefit of U.S. provisional patent application No. 61/169,528, filedApr. 15, 2009. The entire contents of each of these applications areincorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with Government support of Grant No. ES009519,awarded by the National Institutes of Health. The Government has certainrights in the invention.

TECHNICAL FIELD OF THE INVENTION

The present invention relates generally to detection, diagnosis, andmonitoring of allergic inflammation, such as occurs with asthma andother respiratory conditions. The invention more specifically pertainsto use of systemic genotoxicity as a marker for lung inflammation.

BACKGROUND OF THE INVENTION

Asthma affects over 150 million individuals and is clinically diagnosedby a barrage of symptoms, which include wheezing, coughing, andshortness of breath (Akinbami 2011; Miller 2001). Asthma can besubcategorized into two classes: allergic, and non-allergic asthma,which constitute roughly 70% and 30% of cases, respectively. Althoughthere are almost no observable differences in the types of physiologicalchanges that occur between the two subcategories, non-allergicasthmatics incur more severe and more frequent symptoms (Romanet-Manent2002).

Airways of asthmatic individuals are distinguished through structuralmodifications, collectively called airway remodeling that includesbronchiolar inflammation, epithelial sloughing, goblet cell metaplasia,multiplied mucus glands, thickening of the lamina reticularis, increasedairway smooth muscle mass, angiogenesis, and alterations in theextracellular matrix components (Fireman 2003; Hyde 2006). Additionally,B lymphocytes, T lymphocytes, eosinophils, neutrophils, and macrophagesalso migrate to the airways, triggering the release of immunoglobulin E,leukotrienes, prostaglandins, histamines, and other chemical mediatorsleading to airway inflammation (Bradley 1991; Henderson 1996).

In asthmatic individuals, T cells differentiate preferentially towardstype 2 helper T cells (Th2) (Harrington 2005). Th2 cells are thought toinduce asthma through the secretion of many cytokines that activateinflammatory pathways both directly and indirectly (Zimmermann 2003).Notably, Th2 cells secrete IL-13 which triggers STATE activation throughactivation of surface receptors present on eosinophils, mast cells, Blymphocytes, fibroblasts, and airway smooth muscle cells IIs (Chatila2004, Akdis 2011, Jiang 2000, Cohn 2004, Medoff 2008). This activationleads to IgE synthesis, mucus hypersecretion, airway hyperreactivity,and tissue fibrosis (Munitz 2008). Overexpression of IL-13 is necessaryand sufficient to induce non-allergic asthma (Munitz 2008; Akdis 2011;Wills-Karp 1998).

There is a need to identify improved markers for lung inflammation.There is also a need for methods of detecting asthma and differentiatingbetween allergic and non-allergic asthma.

SUMMARY OF THE INVENTION

The invention provides a method for detection of allergic inflammationin a subject. In one embodiment, the method comprises assaying a testsample of peripheral blood from the subject for a marker of DNA damage.The amount of marker present in the test sample is then compared to thatpresent in a control sample. The method can be adapted forquantitatively monitoring the efficacy of treatment of inflammatorydisease in a subject. An elevated amount of marker present in the testsample compared to the control sample is indicative of inflammatorydisease activity, including sub-clinical inflammation. In someembodiments, the method further comprises prescribing treatment forinflammatory symptoms and/or associated disease or modifying an ongoingtreatment strategy on the basis of the assay results.

In one embodiment, the marker of DNA damage is single- and/ordouble-stranded breaks in leukocytes. Such strand breaks can be detectedby immunoassay for γ-H2AX and/or an alkaline comet assay. In anotherembodiment, the marker of DNA damage is oxidative DNA damage inleukocytes, or a marker of nitric oxide oxidative activity (proteinnitrosylation in leukocytes). Oxidative DNA damage can be assayed via anenzyme hOgg1-modified comet assay or by immunoassay for 8-oxoguanine. Anunderlying oxidative process (nitric oxide-mediated oxidation) can beassayed by immunoassay for protein nitrotyrosine. In a furtherembodiment, the marker of DNA damage is micronuclei formation in mature,normochromatic erythrocytes.

The inflammatory disease can be lung inflammation, or inflammation ofthe airway. In one embodiment, the inflammatory disease is a diseaseassociated with interleukin 13 (IL-13) activity, such as allergicinflammation. In one embodiment, the allergic inflammation is allergicasthma. The invention may also be used for detection of other types ofinflammatory disease, such as inflammatory bowel disease, non-immuneintestinal inflammatory disease (diverticulitis, pseudomembranouscolitis), autoimmune diseases (rheumatoid arthritis, lupus, multiplesclerosis, psoriasis, uveitis, vasculitis), or non-immune lung diseases(asthma, chronic obstructive lung disease, and interstitialpneumonitis). In one embodiment, the method can be used to distinguishbetween allergic asthma and non-allergic asthma.

Also provided is a method for monitoring the efficacy of treatment ofinflammatory disease in a subject. The method comprises assaying a testsample of peripheral blood obtained from the subject at a first timepoint for a marker of DNA damage, and again at a second time point, andcomparing the amount of marker present in the test samples obtained atthe first and second time points. A decreased amount of marker presentin the test sample obtained at the second time point compared to thetest sample obtained at the first time point is indicative effectivetreatment of inflammatory disease.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Disease Activity Index (DAI) of DSS Treated vs. Non-TreatedMice. DSS treated mice (n=10) demonstrated significantly higher diseaseactivity indices everyday after Day 4 of Cycle 1 (p<0.001), Day 3 ofCycle 2 (p<0.001), and Day 2 of Cycle 3 (p<0.001) compared tonon-treated mice (n=10). Data are represented as mean±standard error ofthe mean (SEM). †: Blood collection points.

FIG. 2. Mean Olive Tail Moments. At least 150 “comets” were scored permouse in the DSS treated group (n=10) and in the non-treated group(n=10). Data were log transformed before applying statistical tests, andare represented as mean±SEM. *: p<0.05, **: p<0.01.

FIGS. 3A-3B. γ-H2AX foci and Micronucleus Induction. FIG. 3A. Percentpositive cells for γ-H2AX foci in peripheral leukocytes. Presence ofdouble strand breaks was confirmed by immunofluorescence of γ-H2AX.Positive cells contained >4 distinct nuclear foci. Image caption:Positive and negative cell for nuclear foci, 100× magnification. Atleast 125 cells were analyzed per sample. Data are represented asmean±SEM, n=10 per treatment group. **: p<0.01, *: p<0.05 FIG. 3B.Micronucleus induction in peripheral normochromatic erythrocytes. Atleast 4000 normochromatic erythrocytes were counted and scored forpresence of micronuclei. Data are represented as mean±SEM ofmicronucleated normochromatic erythrocytes (MN-NCE) per 1000 NCEs. Imagecaption: MN-NCEs and NCEs, 100× magnification. **: p<0.01, *: p<0.05, bynonparametric one way ANOVA with Dunn's multiple comparison test. ANOVAof normal linear regression showed effect of treatment, cycle oftreatment and interaction of effect of treatment and cycle of treatmentto be significant (p<0.01).

FIGS. 4A-4D. Quantitative Real Time-PCR of Cytokines in PeripheralBlood. Expression levels of cytokines were determined only in DSStreated mice (n=10). Data are represented as mean±SEM of gene expressiondivided by Tbp expression. FIG. 4A. Transcript levels of TNF-α dividedby Tbp. FIG. 4B. Transcript levels of MCP-1 divided by Tbp. FIG. 4C.Transcript levels of IFN-γ divided by Tbp. FIG. 4D. Transcript levels ofTGF-β divided by Tbp. Statistical significance was determined bynon-parametric one-way ANOVAs with Dunn's multiple comparison test. *:p<0.05, **: p<0.01

FIGS. 5A-5D. Systemic Genotoxicity in Mouse Models of MucosalInflammation. Blood was sampled from Gαi2^(−/−), IL-10^(−/−), andcontrol IL-10^(+/+) mice for genotoxicity assays at age 3 months; inaddition, IL-10^(−/−) mice were sampled at age 6 months, when colitis inthis genetic background has progressed to greater clinical activity.FIG. 5A. Representative colon histology (hematoxylin and eosin stainingat indicated magnifications) from Gαi2 and IL-10 mice, both at age 3months. FIG. 5B. Alkaline comet assay with and without hOgg1 incubationwas carried out in peripheral leukocytes. Error bars are SEM, n=6 pergroup. *: p<0.05, **: p<0.01 by Student's unpaired t-test. FIG. 5C.Percent positive cells for γ-H2AX foci in peripheral leukocytes. Errorbars are SEM. *:p<0.05 by Student's unpaired t-test. FIG. 5D. MN-NCEsper 1000 NCEs in peripheral blood. Error bars are SEM. **: p<0.01 byStudent's unpaired t-test.

FIGS. 6A-6C. 8-oxoguanine and Nitrotyrosine Formation in PeripheralLeukocytes and the Colon. FIG. 6A. Representative images of positivestaining for 8-oxoguanine (green, left) and nitrotyrosine (red, right)in leukocytes of DSS-treated wildtype (7 days) and IL-10^(−/−) mice (6months). FIG. 6B. Percent positive cells for 8-oxoguanine andnitrotyrosine staining before and after DSS treated mice (7 days), n=6per group (LEFT) and in IL-10^(−/−) mice (6 months), n=4 per group(RIGHT). *: p<0.05, **: p<0.01 by Student's unpaired t-test. FIG. 6C.Representative images of 8-oxoguanine (green) and nitrotyrosine (red) incolon sections of IL-10^(−/−) mice (6 months) and wildtype mice.

FIG. 7. Disease activity indices (DAIs) of Atm^(−/−), Atm^(+/−), andwildtype mice. Atm^(−/−) mice exhibit higher DAIs (**: p<0.01) byStudent's unpaired t-test compared to Atm^(+/−) and wildtype mice. TwoAtm^(−/−) mice died; one at end of cycle 2, and one at end of cycle 3.Non-treated mice of all genotypes had DAIs of 0 throughout the entirestudy.

FIG. 8A. Mean olive tail moments of peripheral leukocytes with andwithout hOgg1 incubation. A portion of cells were treated with H₂O₂ for20 min as a positive control. Two-way ANOVA with Dunn's multiplecomparison test demonstrate significant (p<0.001) differences betweengenotypes.

FIG. 8B. Percent positive cells for γH2AX in peripheral leukocytes ofAtm^(−/−), Atm^(+/−), and wildtype mice. A portion of cells were treatedwith H₂O₂ for 20 min before staining as a positive control. Two-wayANOVA with Dunn's multiple comparison test demonstrated significanttreatment effects. Genotype differences are shown *: p<0.05, **: p<0.01.

FIG. 9. Micronucleated normochromatic erythrocytes (MN-NCEs) per 1000NCEs. ANOVA of a linear regression model for all three genotypes andtreatment cycle effects were **: p<0.01, *: p<0.05 for Atm^(−/−) versusAtm^(+/−) and wildtype mice unless indicated otherwise.

FIGS. 10A-10I. 8-oxoguanine and nitrotyrosine formation in peripheralleukocytes and the distal colon. FIGS. 10A-10B. 8-oxoguanine (green) andnitrotyrosine (red) staining in peripheral leukocytes, respectively(×100). FIGS. 10C-10D. Percent positive cells for 8-oxoguanine andnitrotyrosine, respectively, in peripheral leukocytes of Atm^(−/−) andwildtype mice. *: p<0.05, **: p<0.01 by Student's unpaired t-test. FIGS.10E-10F. Staining in the distal colon of wildtype mice for 8-oxoguanineand nitrotyrosine, respectively, treated with DSS for 7 days. (×10)FIGS. 10G-10H. Staining in the distal colon of Atm^(−/−) mice for8-oxoguanine and nitrotyrosine, respectively, treated with DSS for 7days. (×10) FIG. 10I. Quantification of 8-oxoguanine and nitrotyrosinestaining in wildtype and Atm^(−/−) mice expressed in pixel area withbrightness value above a set threshold (arbitraty units). **: p<0.01 byStudent's unpaired t-test.

FIGS. 11A-11I. Cytokine panel in peripheral blood by quantitativereal-time PCR. FIGS. 11A-11C. Th1 cytokine panel of TNF-α, MCP-1, andIFN-γ, respectively. FIGS. 11D-11F. IL-12, IL-23, and IL-6,respectively. FIGS. 11G-11I. Th2 cytokine panel of TGF-β, IL-10, andIL-4, respectively. Data are mean expression of gene over expression ofTBP, the internal control gene. *: p<0.05, **: p<0.01 by two-way ANOVAfor genotype comparisons.

FIGS. 12A-12D. Flow cytometric analysis of peripheral leukocytes. FIGS.12A-12B. Percent gated CD69⁺ T-cells (CD4 or CD8α positive) and CD44⁺T-cells, respectively, in peripheral blood. 15,000 cells were countedper mouse. *: p<0.05, **: p<0.01 by Student's unpaired t-test with Welchcorrection for genotype comparisons. FIG. 12C. Baseline CD4⁺ and CD8α⁺peripheral blood T-cells of Atm^(−/−), Atm^(+/−), and wildtype mice.Scale along both X and Y axes ranges from 10⁰ to 10⁴. FIG. 12D. Meanfluorescent intensities of CD44⁺ T-cells in Atm^(−/−), Atm^(+/−), andwildtype mice after cycle 2 (upper panel) and before cycle 3 (lowerpanel). Filled line represents isotype control. Y axes display counts ona scale from 0 to 100. X axes range from 10⁰ to 10⁴.

FIGS. 13A-13D. Genotoxicity to peripheral leukocyte subpopulations.FIGS. 13A-13B. DNA damage as measured by alkaline comet assay with orwithout hOgg1 incubation and γH2AX immunostaining, respectively, inIL-10^(−/−) versus wildtype mice. FIGS. 13C-13D. DNA damage as measuredby alkaline comet assay with or without hOgg1 incubation and γH2AXimmunostaining, respectively, in Gαi2^(−/−) versus wildtype mice. *:p<0.05, **: p<0.01 by two way ANOVA with Dunn's multiple comparisontest. Error bars represent standard error of the mean (SEM).

FIGS. 14A-14C. DNA damage to peripheral lymphoid organs, as determinedby γH2AX immunostaining, alkaline comet assay without hOgg1 incubation,and alkaline comet assay with hOgg1 incubation, respectively, inIL-10^(−/−) mice at 8 weeks of age and 6 months of age versus wildtypemice. *: p<0.05, **: p<0.01 by two way ANOVA with Dunn's multiplecomparison test. Error bars represent SEM.

FIGS. 15A-15B. Genotoxicity to intestinal epithelial cells. DNA damageby alkaline comet assay with and without hOgg1 incubation and by γH2AXimmunostaining, respectively, in IEC's from small and large intestine ofIL-10^(−/−) versus wildtype mice. *: p<0.05, **: p<0.01 by one way ANOVAwith Dunn's multiple comparison test. Error bars represent SEM.

FIGS. 16A-16C. Induction of DNA damage by TNF-α injection. DNA damage toperipheral leukocytes measured by alkaline comet assay with and withouthOgg1 incubation, γH2AX immunostaining, and micronuclei formationmeasured in normochromatic erythrocytes, respectively, in wildtype micebefore and after a single injection of TNF-α or saline. *: p<0.05, **:p<0.01 by one way ANOVA with Dunn's multiple comparison test. Error barsrepresent SEM.

FIGS. 17A-17D. Characterization of cell types with DNA damage afterTNF-α injection. FIGS. 17A-17B. DNA damage measured 1.5 hrspost-injection of TNF-α or saline by alkaline comet assay with andwithout hOgg1 incubation, in peripheral blood subpopulations and inperipheral lymphoid organs, respectively. FIGS. 17C-17D. DNA damage byγH2AX immunostaining in peripheral blood subpopulations and inperipheral lymphoid organs, respectively. *: p<0.05, **: p<0.01 by oneway ANOVA with Dunn's multiple comparison test. Error bars representSEM.

FIGS. 18A-18C. DNA damage after injection of TNF-α and IL-β. DNA damageto peripheral leukocytes measured by alkaline comet assay with andwithout hOgg1 incubation, γH2AX immunostaining, and micronucleiformation measured in normochromatic erythrocytes, respectively, inwildtype mice before and after a single injection of IL-β, TNF-α+IL-β,or saline. *: p<0.05, **: p<0.01 by one way ANOVA with Dunn's multiplecomparison test. Error bars represent SEM.

FIGS. 19A-19B. DNA repair capability in IL-10^(−/−) mice. FIG. 19A.Transcript levels of ATM and XPC relative to the internal control TBP inIL-10^(−/−) versus wildtype mice. FIG. 19B. Protein expression of pATMin CD4 and CD8 T-cells in IL-10^(−/−) versus wildtype mice. *: p<0.05,**: p<0.01 by unpaired Student's t-test. Error bars represent SEM.

FIGS. 20A-20B. DNA damage in IBD patients. DNA damage to peripheralleukocytes as measured by γH2AX immunostaining and by alkaline cometassay with or without hOgg1 incubation in 19 patients with activedisease or in remission.

FIG. 21 Line graph showing IgE concentration assessed via sandwichELISA. **indicates p<, 0.007 n=5 in both IL-13 (upper, lighter line) andWT animals (darker line).

FIGS. 22A-22D IL-13 over-expression induces lung inflammation inasthmatic mice. Representative lung histology Hematoxylin & Eosin (H&E)staining at indicated magnifications. (22A) 10× image of Wild type (WT)lung and Interleukin 13 over expressed mice (22B), both at one monthold. Arrows in (22B) 10× image indicate formation of granuloma metafocisurrounding eosinophilic crystals. 40× image of WT (22C) and (22D) 40×image of IL-13 mice. Arrows in (22D) indicate eosinophil migration,goblet cell metaplasia, and eosinophilic crystal formation in bronchiallumen. n=9 for WT and n=10 for IL-13

FIG. 23. Bar graphs showing inflammatory cell composition of bronchialalveolar lavage fluid (BALF). Differential cell analysis were determinedby light microscopic evaluation n=9 for WT, and n=10 for IL-13animals, * indicates p<0.05, *** indicates p<0.0004 respectivelyanalysis were conducted using two tailed Student's unpaired T-test withMann-Whitney determination.

FIGS. 24A-24G Assessment of cytokine panel in lung mRNA measured byquantitative real-time PCR. Mean expression divided by Gapdh, theinternal control gene. * indicates p<0.01, ** indicates p<0.001,analysis were conducted using two tailed Student's unpaired T-test. n=9for WT animals and n=10 for IL-13 animals.

FIG. 25 Photomicrograph showing staining of markers of genotoxicity andoxidative protein damage in lung tissue as measured byimmunohistochemistry. Markers of double stranded breaks (A-J), reactiveoxygen species (B-K), and inflammation (C-L) induced genotoxicity werestained in WT and IL-13 mice. Lung tissue in IL-13 mice (G-L) exhibitedincreased staining in all genotoxic parameters in comparison to WT mice(A-F). n=9 for WT animals and n=10 for IL-13 animals.

FIGS. 26A-26B Persistent genotoxicity measured via inflammation induced8-oxoguanine and double stranded breaks measured via γH2AX in peripheralblood. A.) Percent positive cells for 8-oxoguanine induction in whiteblood cells. Presence of 8-oxoguanine was confirmed byimmunofluorescence. Positive cells stain brightly green compared to noimmunofluorescent staining for negative cells. White bars indicate Wildtype (WT) animals and black bars indicate IL-13 animals. Data representmean±SEM. Statistical analyses were done using ANOVA testing and Tukey'spost hoc analysis. n=5 in all groups. ** indicates p<0.001. B Assessmentof double strand breaks measured via γH2AX assay, were counted per cellusing fluorescent microscopy before doxycycline administration at Day 0and after doxycycline administration at days 3, 9, 12, 16, 18 and day 21using a linear mixed model to determine genotoxic accumulation overtime. * indicates p<0.02, ** indicates p<0.002 n=5 for WT and IL-13animals.

FIG. 27 IL-13 over-expression induced single stranded breaks andmicronucleated cells in peripheral blood. Assessment of single strandbreaks were measured via comet assay before doxycycline administrationat Day 0 and after doxycycline administration at days 6 (upper panel bargraph). At least 100 olive tail moments were counted via fluorescentmicroscopy and assessed using CASP software. White bars indicate Wildtype (WT) animals and black bars indicate IL-13 animals. Data representmean±SEM. Statistical analyses were done using ANOVA testing and Tukey'spost hoc analysis. * indicates p<0.05 n=5 for WT and IL-13 animals.Number of micronucleated cells per 4000 normorchromatic erythrocytes isplotted as a bar graph in the lower panel. Presence of micronuclei wereconfirmed by light microscope at 100×. White bars indicate Wild type(WT) animals and black bars indicate IL-13 animals. Data representmean±SEM. Statistical analyses were done using ANOVA testing and Tukey'spost hoc analysis. n=9 for WT and n=10 for IL-13.* indicates p<0.05.

DETAILED DESCRIPTION OF THE INVENTION

The invention described herein is based on the discovery that assaysthat detect systemic genotoxicity can be used to detect, diagnose andmonitor inflammation and inflammatory disease, as well as to guide inthe prognosis and selection of treatment. Assays that detect a varietyof endpoints for genotoxicity in peripheral leukocytes have been foundto correlate quantitatively with intestinal inflammation and diseaseseverity. These assays include immunostaining for γ-H2AX, which measuresDNA double strand breaks, and the alkaline comet assay, which measureslevels of DNA single and double strand breaks, as well as oxidative DNAbase damage. DNA damage can also be measured by assaying micronucleusformation in normochromatic erythrocytes. This unexpected discovery ofmarkers of genotoxicity present in circulating leukocytes enablesdetection of inflammation occurring at a localized site with arelatively simple and minimally invasive assay using peripheral blood.

In particular, these assays have been found to be useful in thedetection and monitoring of different types of inflammatory activity. Inaddition to intestinal inflammation, the methods described herein can beused to detect lung inflammation and inflammatory activity associatedwith IL-13 activity, including allergic inflammation and asthma. In oneembodiment, the invention provides methods for the detection,monitoring, and treatment of allergic asthma.

Definitions

All scientific and technical terms used in this application havemeanings commonly used in the art unless otherwise specified. As used inthis application, the following words or phrases have the meaningsspecified.

As used herein, “inflammatory disease” means a clinical disorder inwhich activation of the innate or adaptive immune response is aprominent contributor to the clinical condition.

As used herein, a “sample” from a subject means a specimen obtained fromthe subject that contains blood or blood-derived cells. In a typicalembodiment, the sample is peripheral blood or other sample containingperipheral leucocytes. For example a sample of peripheral leukocytes canbe obtained from fluid of a body cavity, such as pleural, peritoneal,cerebrospinal, mediastinal, or synovial fluid.

As used herein, the term “subject” includes any human or non-humananimal. The term “non-human animal” includes all vertebrates, e.g.,mammals and non-mammals, such as non-human primates, horses, sheep,dogs, cows, pigs, chickens, amphibians, reptiles, etc.

As used herein, “a” or “an” means at least one, unless clearly indicatedotherwise.

Methods of Detecting Inflammatory Activity

The invention provides a method for detection of inflammatory diseaseactivity in a subject. In one embodiment, the method comprises assayinga test sample of peripheral leukocytes from the subject for a marker ofDNA damage. The amount of marker present in the test sample is thencompared to that present in a control sample. An elevated amount ofmarker present in the test sample compared to the control sample isindicative of inflammatory disease.

A control sample is a sample that is representative of a normal ordisease-free condition. In some embodiments, a control is a sampleobtained from a subject known to be normal or free of disease that wouldalter the measured parameters.

The test sample is typically peripheral blood. Alternatively, the testsample can be bone marrow or body cavity fluids (such as peritoneal,pleural, synovial, or cerebrospinal fluids). DNA damage detected inperipheral blood leucocytes correlates with disease activity and withDNA damage in lymphoid organs, such as spleen, mesenteric lymph nodesand peripheral lymph nodes, and in intestinal epithelial cells. Testsamples can be obtained from subjects using conventional means, such asvenipuncture or capillary puncture. Normally the most desirable site forobtaining a blood sample for laboratory testing is from the veins of theantecubital fossa area, i.e. the bend of the elbow of the arm. Acapillary puncture may be used when venipuncture would be too invasiveor not possible. In general, capillary punctures may be done onearlobes, fingertips, heels, or toes, however, heels and toes are not asite of choice, especially in adults. Heel areas are typically used withneonates and younger infants. The site of choice in older children aswell as adults is the distal lateral aspect of the fingertip; usuallythe second or third finger.

One can also assay DNA damage in subpopulations of leukocytes. In someembodiments, the leukocytes are lymphocytes, including subsets oflymphocytes, such as T cells, B cells, and/or NK cells. Alsocontemplated are monocytes, including subsets of monocytes, such asclassical and pro-inflammatory monocytes. As one example, CD4+ and CD8+T-cells, CD19+ B-cells, and CD11b+ macrophages can be separated, such asby magnetic bead separation, for analysis. An increase in the diversityof cell types exhibiting DNA damage can be indicative of more severe oradvanced disease.

In one embodiment, the marker of DNA damage is single- and/ordouble-stranded breaks in the cells to be analyzed. DNA strand breakscan be detected by immunoassay for γ-H2AX and/or an alkaline cometassay. One example of an immunoassay for γ-H2AX is animmune-fluorescence assay using an antibody directed against γ-H2AX thatis directly labeled, or that is used in conjunction with a labeledsecondary antibody. Immunoreactive cells can be imaged using FISHanalysis, wherein cells having at least four distinct foci in thenucleus are considered positive. Apoptotic cells can be distinguishedand excluded from the analysis. An example of an alkaline comet assayfor measuring DNA damage in cells has been described by Olive et al.(Nat. Protocols 2006; 1(1):23-9). Comet images can be visualized, forexample, using fluorescence microscopy, and analyzed using a CASP imageanalysis program. Tail length and fraction of DNA in the tail isrepresented in this assay by the olive tail moment.

In another embodiment, the marker of DNA damage is oxidative DNA damagein the cells to be analyzed. Oxidative DNA damage can be assayed via anenzyme hOgg1-modified comet assay. An example of an hOgg1 comet assayhas been described by Smith et al. (Mutagenesis 2006; 21(3):185-90). Ina further embodiment, the marker of DNA damage is micronuclei formationin mature, normochromatic erythrocytes, as described in the examplesbelow and in Cancer Res. 2009; 69(11):4827-34; and Cancer Res. 2010;70(5):1875-84.

The inflammatory diseases that can be detected include diseasesassociated with IL-13 and inflammation of the airway, including lungdisease. Examples of lung inflammation that can be detected andmonitored include, but are not limited to, asthma, chronic obstructivelung disease, and interstitial pneumonitis. In one embodiment, themethod can be used to differentiate between allergic and non-allergicasthma. The markers of genotoxicity described herein can be used todetect the presence of allergic asthma, which can present with similarsymptoms as non-allergic asthma. Thus, the invention provides a simpleblood test for detection of asthma. Likewise, the invention provides asimple blood test for allergic inflammation.

Those skilled in the art will appreciate additional variations suitablefor the method of detecting inflammation through detection of DNA damagein a specimen, as it provides remote monitoring (peripheral bloodgenotoxicity) to assess disease activity and response to treatment. Thismethod can also be used to monitor levels of these markers in a samplefrom a patient undergoing treatment. The suitability of a therapeuticregimen for initial or continued treatment can be determined bymonitoring marker levels using this method. The extent of genotoxicitypresent in a given patient or test sample can provide a prognosticindicator to guide treatment strategy. Accordingly, one can useinformation about the number and/or quantity of indicators present in asubject to assist in selecting an appropriate treatment protocol. Forexample, treatment of asthma could be monitored by systemic genotoxicityas a surrogate biomarker to quantitatively measure the level ofpersisting disease activity. If disease activity persists above anacceptable level, the clinician would consider increasing the treatmentdose, or changing to a different therapeutic agent.

Kits

For use in the diagnostic applications described herein, kits are alsowithin the scope of the invention. Such kits can comprise a carrier,package or container that is compartmentalized to receive one or morecontainers such as vials, tubes, and the like, each of the container(s)comprising one of the separate elements to be used in the method. Theantibodies of the kit may be provided in any suitable form, includingfrozen, lyophilized, or in a pharmaceutically acceptable buffer such asTBS or PBS. The kit may also include other reagents required forutilization of the reagents in vitro or in vivo such as buffers (i.e.,TBS, PBS), blocking agents (solutions including nonfat dry milk, normalsera, Tween-20 Detergent, BSA, or casein), and/or detection reagents(i.e., goat anti-mouse IgG biotin, streptavidin-HRP conjugates,allophycocyanin, B-phycoerythrin, R-phycoerythrin, peroxidase, fluors(i.e., DyLight, Cy3, Cy5, FITC, HiLyte Fluor 555, HiLyte Fluor 647),and/or staining kits (i.e., ABC Staining Kit, Pierce)). The kits mayalso include other reagents and/or instructions for using antibodies andother reagents in commonly utilized assays described above such as, forexample, flow cytometric analysis, ELISA, immunoblotting (i.e., westernblot), in situ detection, immunocytochemistry, immunohistochemistry.

In one embodiment, the kit provides the reagent in purified form. Inanother embodiment, the reagents are immunoreagents that are provided inbiotinylated form either alone or along with an avidin-conjugateddetection reagent (i.e., antibody). In another embodiment, the kitincludes a fluorescently labeled immunoreagent which may be used todirectly detect antigen. Buffers and the like required for using any ofthese systems are well-known in the art and may be prepared by theend-user or provided as a component of the kit. The kit may also includea solid support containing positive- and negative-control protein and/ortissue samples. For example, kits for performing spotting or westernblot-type assays may include control cell or tissue lysates for use inSDS-PAGE or nylon or other membranes containing pre-fixed controlsamples with additional space for experimental samples.

The kit of the invention will typically comprise the container describedabove and one or more other containers comprising materials desirablefrom a commercial and user standpoint, including buffers, diluents,filters, needles, syringes, and package inserts with instructions foruse. In addition, a label can be provided on the container to indicatethat the composition is used for a specific application, and can alsoindicate directions for use, such as those described above. Directionsand or other information can also be included on an insert which isincluded with the kit.

EXAMPLES

The following examples are presented to illustrate the present inventionand to assist one of ordinary skill in making and using the same. Theexamples are not intended in any way to otherwise limit the scope of theinvention.

Example 1: Intestinal Mucosal Inflammation Leads to SystemicGenotoxicity in Mice

This example demonstrates that genotoxicity is elicited systemically byacute and chronic intestinal inflammation. In this study, genotoxicendpoints were assessed in peripheral leukocytes (DNA single and doublestrand breaks and oxidative DNA damage) and normochromatic erythrocytes(micronuclei) during chemical or immune-mediated colitis. During threeconsecutive cycles of intestinal inflammation induced by dextran sulfatesodium (DSS) administration, genotoxicity to peripheral leukocytes anderythroblasts was detected in both acute and chronic phases ofDSS-induced inflammation. Reactive oxygen species mediated oxidativestress and DNA damage was confirmed with positive 8-oxoguanine andnitrotyrosine staining in peripheral leukocytes. Levels of DNA damagegenerally decreased during remission and increased during treatment,correlating with clinical symptoms and systemic inflammatory cytokinelevels. In Gαi2^(−/−) and IL-10^(−/−) transgenic mice susceptible toimmune-mediated colitis and inflammation-associated adenocarcinoma,similar levels of peripheral leukocyte and erythroblast genotoxicitywere also observed. Moreover, this systemic genotoxicity was observed inmice with subclinical inflammation, which was further elevated in thosewith severe mucosal inflammation. We propose that mucosal inflammation,by eliciting substantial and ongoing systemic DNA damage, contributesearly on to genetic instability necessary for progression toIBD-associated dysplasia and the development of cancer.

Methods

Animals.

C57BL/6Jp^(un)/p^(un) (3 to 4 months), Gαi2^(−/−) (B6/129Sv background,3 months) (9) and IL-10^(−/−) (C3H/HeJBir background, 3 or 6 months)were housed in the UCLA Department of Laboratory and Animal Medicineunder specific pathogen free conditions, autoclaved bedding and food,with standard rodent chow diet, acidified drinking water, and 12:12light:dark cycle. All mice were bred at UCLA except IL-10^(−/−) andC3H/HeJ which were purchased from Jackson Laboratory (Bar Harbor, Me.).

Induction of Chemical Colitis.

Experimental colitis was induced with 3% (w/v) DSS (Fisher Scientific,MW 40,000) dissolved in acidified drinking water (changed daily) adlibitum for 3 cycles. One cycle consisted of 7 days of treated waterfollowed by 14 days of normal drinking water. Acute colitis was definedas a 7 day treatment, and chronic colitis as any further treatmentincluding remission periods. Control animals received sterile acidifiedwater only. Symptoms (weight loss, stool consistency, gross bleeding)were recorded daily for calculation of disease activity index (23).

Blood Collection.

Peripheral blood was collected from experimental mice via thefacial/mandibular vein with a 5 mm lancet (Braintree Scientific,Braintree, Mass.) into EDTA coated collection tubes (BraintreeScientific). For the comet assay, blood was immediately diluted 1:1 inPBS/10% DMSO and frozen at −80° C. until further analysis. Freshlycollected blood was immediately processed for all other assays.Identical blood samples were used for genotoxic endpoints as well as forcytokine expression.

Alkaline Comet Assay.

To detect single and double strand breaks, as well as alkali labilesites in DNA, the alkaline comet assay was performed as describedpreviously (24). Frozen blood was further diluted 1:15 in PBS beforefurther preparation. After lysis and electrophoresis, gels were stainedwith SYBR Gold (Molecular Probes) and visualized under a fluorescentmicroscope (Olympus Ax70, Tokyo, Japan) at 10× magnification. Cometimages were analyzed with the CASP image analysis program(http://casp.sourceforge.net). The olive tail moment, which representsboth tail length and fraction of DNA in the tail, was used for datacollection and analysis, in which apoptotic cells were excluded underpreviously proposed criteria (24).

Determination of Oxidative DNA Damage.

The enzyme hOgg1-modified comet assay was used for determination ofoxidative DNA damage (25). Following lysis, samples were washed in anenzyme wash buffer (40 mM HEPES, 0.1M KCl, 0.5 mM EDTA, 0.2 mg/ml BSA,pH 8.0) then incubated at 37° C. for 10 min in either control (bufferwith no hOGG1) or enzyme treated (buffer with hOGG1) solutions accordingto the manufacturer's recommendations. (New England Biolabs, Ipswich,Mass.). Both control and enzyme treated gels were then placed inelectrophoresis buffer and processed identically to the alkaline cometassay.

Immunofluorescence.

Peripheral blood was incubated in Buffer EL (Qiagen, Valencia, Calif.)on ice to remove erythrocytes. Samples were then processed on coverslipsessentially as described elsewhere (26). Briefly, after fixation,permeabilization, and blocking, cells were incubated with mouseanti-phospho-Histone H2A.X 5139(P) at 1:400, mouse anti-8-oxoguanineclone 413.5 at 1:250, or rabbit anti-nitrotyrosine at 1:200 (all fromUpstate, Temecula, Calif.) followed by FITC-conjugated anti-mouse IgG orRhodamine-conjugated anti-rabbit IgG (Jackson ImmunoResearch, WestGrove, Pa.) at 1:200. Coverslips were mounted with VECTASHIELD with4,6-diamidino-2-phenylindole (Vector Laboratories, Burlingame, Calif.).Images were captured with CytoVision® (Applied Imaging Corporation, SanJose, Calif.) connected to a Zeiss Axioplan 2 microscope. At least 125cells were counted and cells with more than four distinct foci in thenucleus were considered positive for γ-H2AX (26). Apoptotic cells, whichare distinguishable due to presence of 10-fold the number of nuclearfoci in damaged cells (27), were not included in analyses.

Paraffin sections (5 μm) of colons from IL-10^(−/−) and wildtypecontrols were microwaved in 10 mM citrate buffer (pH 6) for 10 min forantigen retrieval, blocked, then incubated with anti-8-oxoguanine oranti-nitrotyrosine followed by secondary antibodies identical to theprocedures described above.

In Vivo Micronucleus Assay.

Micronuclei (MN) formation was determined in peripheral blooderythrocytes to assess chromosomal instability. Similar to a previouslyproposed method (28), 3 μl of whole blood was spread on a microscopeslide and stained in Modified Wright-Giemsa solution (Sigma-Aldrich, St.Louis, Mo.). MN were counted and scored with an Olympus Ax70 (Tokyo,Japan) at 100× following previously proposed criteria (29). At least4000 mature erythrocytes were counted per mouse, and the frequency of MNformation was calculated as number of micronucleated erythrocytes per1000 normochromatic erythrocytes.

RNA Isolation and Quantitative Real-Time PCR.

Total RNA was isolated using QiaAmp RNA Blood Mini Kit (Qiagen)according to manufacturer's instructions. 25 ng/μl of total RNA was usedfor reverse transcription using OligodT (Invitrogen) and Superscript IIIReverse Transcriptase (Invitrogen). 10 ng/μl of cDNA was used forquantitative real time PCR using Taqman Gene Expression Assays (AppliedBiosystems, Foster City, Calif. p/n 4331182) for Tbp (TATA bindingprotein), TNF-α (tumor necrosis factor α), MCP-1 (monocytechemoattractant protein 1, also known as CC chemokine ligand 2, CCL2),IFN-γ (interferon γ), TGF-β (tumor growth factor β) and Taqman GeneExpression Master Mix according to manufacturer's instructions on theABI Prism 7500 sequence detection system (Applied Biosystems). Tbp waschosen as the endogenous control due to its low variability and low tomedium relative abundance in terms of expression in blood (30). Eachmeasurement was performed in triplicate and results were analyzed usingSDS 2.2.1 software (Applied Biosystems). Gene expression was determinedusing the relative standard curve method normalized to Tbp expression.

Statistical Analyses.

Results are expressed as mean±standard error of the mean. Statisticalsignificance was determined by nonparametric one way ANOVAs with Dunn'smultiple comparison post test or a paired Student's t-tests withlog-transformed data for time point comparisons, and defined as p<0.05.ANOVAs of linear regression models were used as appropriate.Calculations were performed with the statistical analysis softwareGraphPad Instat version 3.00 (GraphPad Software, San Diego, Calif.) orR: A language and environment for statistical computing. (R DevelopmentCore Team (2007). R Foundation for Statistical Computing, Vienna,Austria. ISBN 3-900051-07-0, URL http://www.R-project.org).

Results

Evaluation of Experimental Colitis.

The disease activity index (DAI) is the average combined score of weightloss (0-4), stool consistency (0-4), and bleeding (0-4), used to scoreclinical symptoms (23). DSS-treated mice demonstrated rectal bleedingstarting day 4 in cycle 1, represented by the increase in the DAIcompared to non-treated animals (FIG. 1). However, the onset of severesymptoms came earlier in the second and third cycles of treatment due tochronic inflammation, even after 14 day remission periods. Bleeding anddiarrhea ceased as soon as treatment was stopped during remission and nomortalities were observed after three cycles of treatment. Food intakewas also not affected throughout the study and significant weight losswas only apparent during the end of the second and third cycle.

DSS Treatment Causes DNA Single and Double Strand Breaks in PeripheralLeukocytes.

Single and double strand breaks as well as alkali-labile sites in DNA ofperipheral leukocytes were measured in terms of the mean olive tailmoment with the alkaline comet assay (FIG. 2). While mean olive tailmoments of non-treated mice remained low throughout each cycle oftreatment, DSS treated mice demonstrated significantly higher olive tailmoments at the end of each cycle (p<0.01). After each remission periodof 14 days, levels of DNA damage decreased most likely due to DNArepair. The hOgg1 modified alkaline comet assay was also used to detectoxidative base damage. Ogg1 primarily recognizes and removes8-oxoguanine through a base excision repair pathway, as well as8-oxoadenine, fapy-guanine, and methyl-fapy-guanine (31). Mean olivetail moments were higher when incubated with hOgg1 after treatmentcycles in treated mice compared to hOgg1 incubated non-treated mice(p<0.05), indicating presence of oxidized base damage. When compared tolevels before cycle 1, hOgg1 incubated DNA from DSS-treated mice weresignificantly higher at every following time point (p<0.01). Levels ofDNA damage increased with each treatment cycle especially when includingoxidative base damage, indicating damaging effects of acute and moresignificantly, chronic inflammation. A small number of apoptotic cellswith extensive DNA fragmentation were apparent after treatment cycles,however were not included in calculation of mean olive tail moments.

Presence of DNA double strand breaks alone was confirmed withimmunofluorescence of γ-H2AX (FIG. 3A). In response to double strandbreaks, histone 2AX is phosphorylated (γ-H2AX) in a 2-Mbp regionflanking the double strand break within 15 minutes (27). Percentage ofcells positive for nuclear foci increased dramatically in the DSStreated group after the first 7 day acute treatment (p<0.01) compared tonon-treated animals. Although not as dramatic, percent positive cellsremained elevated over non-treated animals until end of treatment(p<0.05). Efficient DNA double strand break repair may be activated,decreasing the presence of foci in chronic inflammation due to theseverely damaging nature of double strand breaks compared to oxidativebase damage or single strand breaks.

DSS-Induced Inflammation is Clastogenic to Erythroblasts.

The in vivo micronucleus (MN) assay was carried out in maturenormochromatic erythrocytes circulating in the peripheral blood todetermine chromosomal damage to erythroblasts (FIG. 3B). The incidenceof micronuclei is commonly used as an index of cytogenetic damage,including chromosome breaks, spindle abnormalities, or structurallyabnormal chromosomes; most frequently in erythroblasts/erythrocytes fromperipheral blood or bone marrow (29). Mature micronucleatednormochromatic erythrocytes represent the final developmental stage oferythroblasts containing micronuclei stemming in the bone marrow, andthus permit the study of both the generation and elimination ofmicronucleated erythrocytes (32).

Micronucleus formation was significantly induced after the first cycleof treatment in DSS treated animals (p<0.01) compared to non-treatedanimals, and was further induced after the second and third cyclescompared to both non-treated animals, and levels before cycle 1(p<0.01). Similar to patterns seen in the results of the alkaline cometassay, micronuclei formation decreased after remission periods, andincreased after each cycle of treatment. This indicates clearance ofmicronucleated erythrocytes by the spleen followed by induction duringtreatment periods. Starting at the before cycle 3 time point,micronucleated erythrocyte levels were slightly elevated even innon-treated animals, most likely due to the effects of repeated blooddraws and consequentially high rate of erythopoiesis.

DSS Treatment Modulates mRNA Expression of Cytokines in PeripheralBlood.

Systemic inflammation due to DSS treatment was demonstrated by cytokinegene expression in the peripheral blood of treated animals. Leukocytescirculating in the periphery mounted a strong Th1 response characterizedby up-regulation of TNF-α, MCP-1 (CCL2), and IFN-γ particularly afterthe first cycle of treatment (FIG. 4). TNF-α transcript levels followedDNA damage patterns of increasing after each 7 day treatment cycle, thendecreasing after each 14 day remission period. MCP-1 and IFN-γtranscript levels increased after the first cycle, then decreased afterthe remission period, where they remained low until rising once again inthe third cycle; demonstrating a delayed secondary induction compared toTNF-α. TGF-β, an anti-inflammatory cytokine, was also modulatedsimilarly to MCP-1 and IFN-γ. DSS treatment induces both a Th1 responseas well as an anti-inflammatory response over the acute and chronicphases of treatment in the peripheral blood.

DNA Damage is Observed in Genetic Models of Mucosal Inflammation.

In order to further determine whether systemic genotoxicity is a generalconsequence of colitis, we measured DNA damage in two genetic models ofmucosal inflammation without the use of DSS. We examined Gαi2^(−/−) miceat age 3 months (chronic active inflammation with neoplastic changes incolon), and IL-10^(−/−) at age 3 and 6 months (in which mice havesubclinical disease with minimal histologic inflammation, and activedisease and inflammation with mild epithelial hyperplasia, respectively)(FIG. 5A). Single and double DNA strand breaks were significantly higher(p<0.01) in both Gαi2^(−/−) mice compared to age-matched Gαi2^(+/−) micewithout clinical symptoms and in IL-10^(−/−) mice with sub-clinicalinflammation compared to age-matched IL-10^(+/+) mice using the cometassay (FIG. 5B). We then hypothesized that IL-10^(−/−) mice with severemucosal inflammation would have greater DNA damage than those withsub-clinical inflammation. These mice indeed demonstrated higher levelsof strand breaks than IL-10^(−/−) mice with sub-clinical inflammation(p<0.01), comparable to those seen in Gαi2^(−/−) mice. Oxidative basedamage, however, seemed only apparent in Gαi2 mice as measured by hOgg1incubation. DNA double strand breaks measured by γ-H2AXimmunofluorescence (FIG. 5C) were also elevated in both Gαi2^(−/−) andIL-10^(−/−) compared to Gαi2^(+/−) and IL-10^(+/+) mice, respectively,though only statistically significant in Gαi2^(−/−) mice (p<0.05), andin IL-10^(−/−) mice with severe mucosal inflammation (p<0.05). Finally,micronucleus induction in erythroblasts were also significantly elevatedin Gαi2^(−/−) mice compared to Gαi2^(+/−) mice (p<0.01), and elevatedbut not statistically significantly elevated in IL-10^(−/−) versusIL-10^(+/+) mice (FIG. 5D). Systemic genotoxicity can therefore beincurred by several modes of inflammation, independent of DSSadministration.

Intestinal Inflammation Induces ROS Mediated Oxidative Stress and DNADamage.

To determine potentially causative species of oxidative stress due tointestinal inflammation, peripheral leukocytes from DSS treated mice (7days, 3% w/v) and IL-10^(−/−) mice (6 months) were isolated and stainedfor 8-oxoguanine or nitrotyrosine (FIGS. 6A and B). 8-oxoguanine is anoxidative DNA lesion formed by reaction of hydroxyl radicals, metalhyrdroperoxides, or peroxynitrite with DNA, causing G:C to T:Atransversions during replication (33). Nitrotyrosine is a biochemicalmarker for NO-induced peroxynitrite formation involving reactions withreactive oxygen and nitrogen species resulting in nitrative damage toproteins (34). DSS-induced inflammation caused a significant increase inboth 8-oxoguanine and nitrotyrosine (p<0.01) in peripheral leukocytes,as did those isolated from IL-10^(−/−) mice (p<0.05). Colon sectionsfrom IL-10^(−/−) mice also demonstrated 8-oxoguanine residues mostly inthe nuclei of the surface epithelial cells as well as in infiltratinginflammatory cells within or near the lamina propria as “focus” like orpan-nuclear staining (FIG. 6C). Nitrotyrosine residues were also presentin the cytoplasm of epithelial cells and inflammatory cells, whereas noimmunoreactivity was observed in wildtype mice.

Discussion

Previous studies have established the role of inflammation-derivedoxidative DNA damage to inflammatory and surrounding epithelial cellsonly at the localized sites of inflammation in the colon. Our studydemonstrates for the first time that this damage extends beyond the siteof inflammation to circulating leukocytes and erythroblasts in the bonemarrow, manifesting a systemic effect, and correlating to oxidativedamage found in inflammatory tissue. Genotoxicity to peripheralleukocytes was evident in terms of both single and double strand breaksto DNA accompanied by oxidative base damage while chromosomalaberrations took place in erythroblasts. Such findings were observedboth in acute and chronic phases of chemical colitis induced by DSSadministration, and in untreated Gαi2^(−/−) and IL-10^(−/−) miceundergoing spontaneous immune colitis. Moreover, in IL-10^(−/−) mice,which are notable for a delayed onset of colitis, genotoxicity wasfurther elevated in mice which had proceeded to a state of clinicallyactive colitis versus those with sub-clinical inflammation. Markers ofreactive oxygen species (ROS) derived oxidative stress demonstratedpresence of 8-oxoguanine and nitrotyrosine in peripheral leukocytes ofDSS treated mice and IL-10^(−/−) mice, representing possible mechanismsof genotoxicity and correlating to oxidative damage seen in the colon.Accordingly, the present study reveals that systemic genotoxicity is aprevalent feature of subclinical, acute, and chronic colitis.

In DSS-treated mice, repair of DNA damage was observed during remissionperiods, represented by a decrease in damage markers. However, theextent of repair appeared slightly less in the last remission due toincreasing severity of chronic inflammation. Despite increasing severityof inflammation, double strand breaks remained only slightly elevatedover non-treated animals, which may imply efficient repair in comparisonto single strand breaks and oxidative damage. DSS administration alsoinduced systemic distribution of cytokines, as evidenced by modulationof transcript levels in peripheral blood. Interestingly, TNF-α wasup-regulated during treatment, and down-regulated during remission,mirroring patterns seen in genotoxicity to leukocytes. Similar toprevious cytokine studies in the colons of DSS treated mice (20),features of both Th1 and Th2 activity were observed systemically in theperipheral blood, leading to chronic activation of immune cells. Thedecrease in MCP-1 and IFN-γ expression after the first cycle oftreatment may be explained by a shift towards higher expression of Th2cytokines and a decrease in selective Th1 cytokines, as recentlydocumented (35) in DSS treated mice. Chronic DSS treatment mimics IBDwith similar cytokine profiles demonstrating dysregulated and imbalancedimmunologic responses to commensal bacterial antigens. Dysregulated andpolarized cytokine production play key roles in enhancing chronicinflammation and tumorigenesis through signaling release of pro-tumormediators (36).

The present study shows that both chemical and genetic/immune models ofinflammation-mediated carcinogenesis not only parallel the inflammationto dysplasia to cancer sequence of human IBD, but also manifestinflammation-associated oxidative stress in the colon as seen in UC andCrohn's disease. Unlike other colitis-associated neoplasia modelsutilizing genotoxic colon carcinogens as initiators of neoplasia(azoxymethane or 1,2-dimethylhydrazine), DSS itself is not a mutagen norgenotoxic (37). However, it has been shown to both directly andindirectly activate macrophages and other inflammatory cells (16, 38), acentral feature of genetic models of immune colitis (8-11). Thus,carcinogenesis arising in these settings is solely a manifestation ofchronic inflammation. The prominent mucosal and systemic activation ofmacrophages, neutrophils, eosinophils, and other effectors inDSS-induced colitis, genetic immune colitis (and in active disease ofpatients with IBD) is a potential source of oxidative stress. This maycause oxidative and nitrative damage locally through oxidative burst,and through release of cytokines that induce receptor-mediated reactiveoxidative species production by target cells. Microsatellite instabilitywas identified in tumors in colons of DSS-treated wildtype mice, andmore so in Msh2^(−/−) mice (39). DSS treatment also induced 8-oxoguanineresidues in mouse colonic mucosa (22), suggesting oxidative damagedirectly at the site of inflammation. Notably, this observed systemicgenotoxicity is a secondary effect of DSS treatment, namely theconsequence of systemic inflammation and inflammation-associatedoxidative stress. In agreement with these findings, we have demonstrated8-oxoguanine and nitrotyrosine formation in the surface epithelium andinflammatory infiltrate of IL-10^(−/−) colons as well as in peripheralblood of IL-10^(−/−) and DSS treated wildtype mice, indicating systemicpresence of peroxynitrite and reactive oxygen and nitrogen species.

We envision two, non-exclusive processes linking local inflammation andsystemic genotoxicity. First, locally activated innate immune cells mayrelease reactive species inducing formation of other reactive speciessuch as hydroxyl radicals and NO-derived peroxynitrite, damagingemigrating resident leukocytes, that then circulate into the periphery.Alternatively, inflammatory cytokines achieve biologically significantsystemic levels, upon which they induce autonomous, cytokine-receptormediated production of free radicals (and genotoxic damage) in remoteleukocyte populations. Both scenarios are possible, as we observedpro-inflammatory cytokines throughout DSS treatment in the peripheralblood, and oxidative DNA damage and nitrotyrosine formation incirculating leukocytes. Similarly, micronucleus formation in theerythroblasts of the bone marrow in our study may have been a result ofactivated T-cells that are part of the normal recirculating lymphocytepool circulating into the bone marrow, and leading to oxidative damage.Accumulation of single and double strand breaks can sequentially lead tochromosome breaks and micronuclei formation (40).

In addition, biologic processes affected by inflammation may alsodetermine the fate of cells bearing genotoxic damage. Since inflammatorymediators elicit both epithelial cell proliferation and anti-apoptoticsignals, epithelial cells in chronic inflammation are at particular riskto DNA damage leading to fixation of mutations that may not be properlyrepaired and removed (22). In DSS colitis, oxidative DNA damage waspositively correlated with apoptosis in the small intestine but not thelarge intestine (41). This biologic difference may contribute to therelative susceptibility to cancer progression in the large intestine.While the mechanism of this differential induction of apoptosis isuncertain, genotoxic stress induces expression of ligands for the NKG2Dreceptor (42). This receptor is differentially expressed on residentCD8⁺ T cells and natural killer cells of the small versus largeintestine, and is a potent inducer of anti-epithelial cytotoxicity inthis intestinal region (43). Finally, the possibility of reciprocalregulation of inflammation and DNA repair pathway elements is anemerging area of investigation (44).

In summary, intestinal inflammation is associated with systemicgenotoxicity through single and double DNA strand breaks, oxidative DNAdamage, protein nitration, and micronucleus formation. We propose thatelements of the inflammatory response including ROS derived oxidativestress are responsible for the observed systemic genotoxicity. Previousstudies have observed oxidative base damage, microsatellite instability,and gene mutations directly in the colonic mucosa of both human IBD andexperimental murine colitis. Here, we highlight that systemic DNA damageaccompanied by systemic inflammation is an early event involved in thepromotion of genetic instability. Such systemic genotoxicity may be abiologically relevant and sensitive biomarker of one processcontributing to inflammation-associated carcinogenesis.

REFERENCES CITED IN EXAMPLE 1

-   1. Loftus E V. Gastroenterology 2004; 126(6):1504-17.-   2. Ekbom A, Helmick C, Zack M, Adami H O. N Engl J Med 1990;    323(18):1228-33.-   3. Xie J, Itzkowitz S H. World J Gastroenterol 2008; 14(3):378-89.-   4. Chu F F, et al. Cancer Res 2004; 64(3):962-8.-   5. Maggio-Price L, et al. Am J Pathol 2005; 166(6):1793-806.-   6. An G, Wei B, Xia B, et al. J Exp Med 2007; 204(6):1417-29.-   7. Greten F R, et al. Cell 2004; 118(3):285-96.-   8. Beatty P L, Plevy S E, Sepulveda A R, Finn O J. J Immunol 2007;    179(2):735-9.-   9. Rudolph U, et al. Nat Genet. 1995; 10(2):143-50.-   10. McPherson M, et al. Am J Physiol Gastrointest Liver Physiol    2008.-   11. Nemetz N, et al. Int J Cancer 2008; 122(8):1803-9.-   12. Popivanova B K, et al. J Clin Invest 2008; 118(2):560-70.-   13. O'Mahony L, et al. Aliment Pharmacol Ther 2001; 15(8):1219-25.-   14. Erdman S E, et al. Am J Pathol 2003; 162(2):691-702.-   15. Takedatsu H, et al. Gastroenterology 2008.-   16. Okayasu I, et al. Gastroenterology 1990; 98(3):694-702.-   17. Cooper H S, et al. Carcinogenesis 2000; 21(4):757-68.-   18. Lennard-Jones J E, et al. Gut 1990; 31(7):800-6.-   19. Dieleman L A, et al. Gastroenterology 1994; 107(6):1643-52.-   20. Dieleman L A, et al. Clin Exp Immunol 1998; 114(3):385.-   21. Ohkusa T, et al. Digestion 1995; 56(2):159-64.-   22. Meira L B, et al. J Clin Invest 2008; 118(7):2516.-   23. Murthy S N, et al. Dig Dis Sci 1993; 38(9):1722-34.-   24. Olive P L, Banath J P. Nat Protocols 2006; 1(1):23-9.-   25. Smith C C, et al. Mutagenesis 2006; 21(3):185-90.-   26. Goldstine J V, et al. DNA Repair 2006; 5(4):432-43.-   27. Muslimovic A, et al. Nat Protocols 2008; 3(7):1187.-   28. Schmid W. The micronucleus test for cytogenetic analysis.    Chemical mutagens Principles and methods for their detection New    York:Plenum 1976:31-53.-   29. Hayashi M, et al. Mutat Res 1994; 312(3):293-304.-   30. Lossos I S, et al. Leukemia; 17(4):789-95.-   31. Bjoras M, et al. EMBO J. 1997; 16(20):6314-22.-   32. Steinheider G, et al. Cell Biol Toxicol 1986; 2(1):197-211.-   33. Pinlaor S, et al. Carcinogenesis 2004; 25(8):1535-42.-   34. Liu J S, et al. Am J Pathol 2001; 158(6):2057.-   35. Alex P, et al. Inflamm Bowel Dis 2009; 15(3):341-52.-   36. Johansson M, et al. Immunol Rev 2008; 222(1):145-54.-   37. Mori H, et al. Nutr Cancer 1984; 6(2):92-7.-   38. Shintani N, et al. Scand J Immunol 1997; 46(6):581-6.-   39. Kohonen-Corish M R J, et al. Cancer Res 2002; 62(7):2092-7.-   40. Obe G, et al. Mutat Res 2002; 504(1-2):17-36.-   41. Hong M Y, et al. Exp Biol Med 2005; 230(7):464-71.-   42. Gasser S, et al. Nature 2005; 436(7054):1186-90.-   43. Meresse B, et al. J Exp Med 2006; 203(5):1343.-   44. Coscoy L, Raulet D H. Cell 2007; 131(5):836-8.

Example 2: Elevated DNA Damage and Persistent Immune Activation in AtmDeficient Mice with Dextran Sulfate Sodium-Induced Colitis

This example describes the systemic DNA damage and immune response toinduced experimental colitis in mice deficient in ATM, a DNAdouble-strand break recognition and response protein. To determine theeffect of Atm deficiency in inflammation, we induced experimentalcolitis in Atm^(−/−), Atm^(+/−) and wildtype mice via dextran sulfatesodium (DSS) administration. Atm^(−/−) mice had higher disease activityindices and rates of mortality compared to heterozygous and wildtypemice. Systemic DNA damage and the immune response were characterized inperipheral blood throughout and after three cycles of treatment.Atm^(−/−) mice demonstrated increased sensitivity to levels of DNAstrand breaks in peripheral leukocytes, as well as micronuclei formationin erythroblasts compared to heterozygous and wildtype mice, especiallyduring remission periods and after the end of treatment. Markers ofreactive oxygen and nitrogen species-mediated damage, including8-oxoguanine and nitrotyrosine were present in both the distal colon andin peripheral leukocytes, with Atm^(−/−) mice manifesting more8-oxoguanine formation than wildtype mice. Atm^(−/−) mice demonstratedgreater upregulation of inflammatory cytokines, and significantly higherpercentages of activated CD69⁺ and CD44⁺ T-cells in the peripheral bloodthroughout treatment. ATM therefore may be a critical immunoregulatoryfactor dampening the deleterious effects of chronic DSS-inducedinflammation, necessary for systemic genomic stability and homeostasisof the gut epithelial barrier.

Methods

Animals.

Adult Atm^(−/−) mice crossed into the parental C57BL/6J p^(un)/p^(un)background as previously described (18), heterozygous (Atm^(+/−)p^(un)/p^(un)), and wildtype control mice (Atm^(+/+) p^(un)/p^(un)), 12to 16 weeks old, were housed in a specific pathogen free facility fed astandard rodent chow diet, provided acidified drinking water, and 12:12light:dark cycle. Food, bedding, and water were autoclaved. Allexperimental procedures were in accordance with the UCLA Animal ResearchCommittee guidelines.

Induction of Experimental Colitis.

Acute and chronic experimental colitis was induced by administering 3%(w/v) DSS (MP Biomedicals, MW 40,000) dissolved in sterile acidifieddrinking water ad libitum for 3 cycles. One cycle of treatment consistedof 7 days of treated water followed by 14 days of normal drinking water.Water was changed daily and symptoms including weight loss, stoolconsistency, and gross bleeding were also recorded for calculation ofthe disease activity index (DAI), as described further elsewhere (19).Briefly, a score ranging from 0-4 was assigned for each measure (weightloss (0-15% loss), stool consistency (normal to diarrhea), and blood instool (no blood to gross bleeding)), and the average of these scores wasrecorded as the DAI. Mice were monitored for 31 days after the end oftreatment.

Blood Collection.

Peripheral blood was collected via the mandibular vein with a 5 mmlancet (Braintree Scientific, Braintree, Mass.) into EDTA coated tubes(Braintree Scientific). Blood was collected before and right after eachseven day treatment of DSS, for three cycles and at two and four weeksafter the end of the three cycles. For the comet assay, blood wasimmediately diluted 1:1 in RPMI/10% DMSO and immediately frozen at −80°C. until further analysis. Freshly collected blood was immediatelyprocessed for all other assays. Identical samples were used forgenotoxicity endpoints as well as for cytokine expression or flowcytometry, allowing each animal to serve as its own control.

Alkaline Comet Assay.

To detect DNA strand breaks, as well as alkali labile sites, thealkaline comet assay was performed and analyzed as described elsewhere(1, 20). The olive tail moment, which represents both tail length andfraction of DNA in the tail, was used for data collection and analysis,in which apoptotic cells were excluded under previously proposedcriteria (20).

Determination of Oxidative DNA Damage.

The enzyme hOgg1-modified comet assay was used and carried outidentically as previously described (1).

Immunofluorescence.

Peripheral blood was incubated in Buffer EL (Qiagen, Valencia, Calif.)to remove erythrocytes. Samples were then processed on coverslips andstained with anti-phospho-Histone H2A.X S139(P), mouse anti-8-oxoguanineclone 413.5, or rabbit anti-nitrotyrosine (Millipore, Temecula, Calif.)as described previously (1, 21). At least 125 cells were counted andcells with greater than four distinct foci in the nucleus wereconsidered positive for γ-H2AX (21). Apoptotic cells, distinguishabledue to the presence of 10-fold the number of nuclear foci in damagedcells (22), were not included in analyses.

Paraffin sections (5 μm) of colons from Atm^(−/−) and wildtype controlswere microwaved in 10 mM citrate buffer (pH 6) for 10 min for antigenretrieval, blocked, then incubated with anti-8-oxoguanine oranti-nitrotyrosine followed by secondary antibodies identical toprocedures described above. Images were captured with CytoVision®(Applied Imaging, UK) and staining was quantified using ImageJ software(23).

In Vivo Micronucleus Assay.

Micronuclei (MN) formation was determined in peripheral blooderythrocytes to assess chromosomal instability as previously described(1). At least 4000 mature erythrocytes were counted per animal, and thefrequency of MN formation was calculated as the number of micronucleatederythrocytes per 1000 normochromatic erythrocytes.

RNA Isolation and Quantitative Real-Time PCR.

Total RNA was isolated using QiaAmp RNA Blood Mini Kit (Qiagen)according to manufacturer's instructions. 25 ng/μl of total RNA was usedfor reverse transcription using OligodT (Invitrogen) and Superscript IIIReverse Transcriptase (Invitrogen). 10 ng/μl of cDNA was used forquantitative real time PCR using Taqman Gene Expression Assays (AppliedBiosystems, Foster City, Calif.) for TBP (TATA box binding protein),TNF-α (tumor necrosis factor-alpha), MCP-1 (monocyte chemoattractantprotein-1), IFN-γ (interferon-gamma), TGF-β (transforming growthfactor-beta), IL-4 (interleukin-4), IL-10 (interleukin-10), IL-6(interleukin-6), IL-17 (interleukin-17), IL-23 (interleukin-23), IL-12(interleukin-12) according to manufacturer's instructions on the ABIPrism 7500 sequence detection system (ABI). TBP was chosen as theendogenous control due to its low variability and low to medium relativeabundance in expression in blood (24). Each measurement was performed intriplicate and results were analyzed using SDS 2.2.1 software (ABI).Quantification of gene expression was determined using the relativestandard curve method normalized to TBP expression.

Flow Cytometry.

T cell populations were characterized for activation status (CD69 andCD44) and CD4 or CD8α expression using flow cytometry. Erythrocytes wereimmediately lysed with BD PharmLyse Lysis Buffer (BD Biosciences, SanDiego, Calif.). After washing with Stain Buffer with 0.2% BSA (BD),cells were stained with FITC conjugated Hamster Anti-Mouse CD69, FITCconjugated Rat Anti-Mouse/Human CD44, R-PE conjugated Rat Anti-MouseCD4, PerCP Rat Anti-Mouse CD8α, or appropriate negative isotype controls(BD Biosciences) for 30 min at 4° C. Cells were then washed and analyzedusing BD FACScan. Fluorescence intensity was normalized to eachrespective isotype control antibody and data were analyzed withCellQuest®(BD Biosciences). Dead cells were excluded by gating onforward/side scatter. Marker expression was recorded either as percentpositive of the absolute count of total T cells, or by medianfluorescence intensity if the control and marker populations overlapped.

Statistical Analyses.

Results (error bars) are expressed as mean±standard error of the mean(SEM) with n=10 mice per genotype. Statistical significance wasdetermined by nonparametric one-way/two-way ANOVAs with Dunn's multiplecomparison post test or paired Student's t-tests with log-transformeddata for time point comparisons, defined as p<0.05. ANOVAs of linearregression models were used as appropriate. Genotoxicity assays and flowcytometry were repeated twice. Calculations were performed with GraphPadInstat 3.00 (Graph Pad Software, San Diego, Calif.) or R: a language andenvironment for statistical computing (Vienna, Austria)(25).

Results

Atm^(−/−) Mice Show Elevated Sensitivity to DSS Treatment.

Mice were monitored daily for measurement of the disease activity index(DAD; an average score taking into account weight loss, stoolconsistency, and presence of blood in the stool, with a maximum score of4. After an acute 7 day exposure to DSS, Atm^(−/−) mice had a mildlyhigher disease activity index compared to wildtype and heterozygous mice(FIG. 7). Differences in symptom severity became more apparent towardsthe end of the second and third cycles (**: p<0.01), during chronicinflammation. Heterozygous and wildtype mice had similar DAIs throughoutthe study, indicating a lack of a gene dosage effect. In addition,Atm^(−/−), Atm^(+/−), and wildtype mice without DSS treatment had DAIsof 0 throughout the entire study, demonstrating no baseline clinicalsymptoms. Two out of ten Atm^(−/−) mice died due to severe symptoms andrectal prolapse; one at the end of the second, and one at the end of thethird cycle. All other mice survived the entire treatment. Duringremission periods, no signs of weight loss or persistent diarrhea werepresent in all genotypes. Surviving mice were also followed for fourweeks after the end of the third cycle, however no symptoms wereevident.

Elevated Systemic Genotoxicity in Atm^(−/−) Mice.

Since Atm^(−/−) mice are defective in DNA double strand break repair andhave higher levels of cellular oxidative stress (26), we hypothesizedthat inflammation-induced DNA damage would be more pronounced.Sensitivity to treatment was therefore assessed in terms of genotoxicityto peripheral leukocytes, a systemic measure of DNA damage. DNA strandbreaks as well as alkali-labile sites, represented by the olive tailmoment, increased in wildtype mice after the first cycle (p<0.001) (FIG.8A). Damage was repaired during the first remission period, andsuccessively increased after the second cycle until 2 weeks after thelast cycle of treatment, before repair of damage was seen again.Oxidative base damage, as measured by incubation with hOgg1, was notsignificant in wildtype mice until after the third cycle of treatment.

On the other hand, DNA strand breaks successively increased in Atm^(−/−)mice with treatment, regardless of the remission periods. Olive tailmoments were significantly higher in Atm^(−/−) mice especially after thesecond and third cycles of treatment compared to wildtype mice(p<0.001). Oxidative base damage was also more apparent in Atm^(−/−)mice, and more so after the end of the second cycle of treatment and upto 4 weeks after the end of the last treatment (p<0.001). Atm^(−/−) micetherefore incur more DNA damage than wildtype mice, especially inchronic inflammation.

DNA double-stranded breaks alone were confirmed in peripheral leukocytesvia immunofluorescence of γ-H2AX (FIG. 8B). Phosphorylation of histone2AX, or γ-H2AX, occurs in response to double-stranded breaks, over a2-Mbp region flanking the break site (22). ATM and other ATM-likekinases are responsible for this phosphorylation. Double-stranded breakswere generally more prevalent in lymphocytes than in other mononuclearcells types, and peaked after the second cycle and during the followingremission period for all three genotypes. Atm^(−/−) mice hadsignificantly higher levels of double-stranded breaks during all threeremission periods than wildtype mice (p<0.05), also seen with the cometassay. Lack of repair of double-stranded breaks was once again evident 2and 4 weeks after the end of treatment in Atm^(−/−) mice, possiblyrepresenting incomplete healing of the epithelial barrier, and prolongedeffects of chronic inflammation. Heterozygous mice demonstrated similarpatterns of γ-H2AX formation to wildtype mice throughout treatment andremission periods. A slight but non-significant increase indouble-strand break formation, however, was seen over wildtype mice 2weeks after the end of treatment.

Micronucleus formation in erythroblasts was measured as micronucleatedmature erythrocytes in the peripheral blood. Toxicity of inflammationwas evident as early as after the acute 7 day treatment of DSS, and moreseverely so in Atm^(−/−) mice (FIG. 9). Micronucleus induction wassignificantly higher in Atm^(−/−) mice at every point of bloodcollection throughout treatment, and up to 4 weeks afterwards comparedto both wildtype and heterozygous mice. Similarly to γH2AX fociformation, heterozygous mice demonstrated higher levels of micronucleusformation only at 2 and 4 weeks after the end of treatment compared towildtype mice, further indicating the importance of ATM during chronicinflammation. Increased sensitivity of Atm^(−/−) mice to chromosomalaberrations in the bone marrow may be due to continual induction ofdamage to erythroblasts in the bone marrow, or a defect in clearance ofmicronucleated erythrocytes.

Increased 8-Oxoguanine Formation in Peripheral Blood and Colon Tissue.

The presence of inflammation-derived reactive oxygen and nitrogenspecies potentially causative for the observed DNA strand breaks as wellas micronucleus formation was measured in the form of 8-oxoguanine inDNA and nitrotyrosine in proteins of peripheral leukocytes and in thedistal colon (FIG. 10). 8-oxoguanine is a DNA lesion caused by thereaction of oxidative reactive species such as hydroxyl radicals withDNA causing G:C to T:A transversions during replication (27), andnitrotyrosine is formed from NO-induced peroxynitrite reacting alongwith other reactive species to tyrosine residues of proteins (28).Wildtype mice alone demonstrated significant increases after an acute 7day exposure to DSS in both 8-oxoguanine and nitrotyrosine formation inperipheral leukocytes (p<0.01). Atm^(−/−) mice also demonstratedsignificant increases in 8-oxoguanine (p<0.05) and nitrotyrosineformation (p<0.05) after 7 days of DSS treatment, however, only8-oxoguanine formation was significantly higher in Atm^(−/−) compared towildtype mice at the end of treatment (p<0.05). Both 8-oxoguanine andnitrotyrosine were also evident in surface epithelial cells proximal toand in the villous crypts closest to the intestinal lumen and ininflammatory cells of the distal colon (FIGS. 10E-10H). Staining for8-oxoguanine localized in the nucleus while nitrotyrosine was evident inboth the nucleus and cytoplasm of damaged cells. Staining for8-oxoguanine was more prominent in the Atm^(−/−) compared to wildtypemice (p<0.01), while nitrotyrosine levels were similar in both genotypes(FIG. 10I).

Persistent Immune Response in Atm^(−/−) Mice.

As a possible explanation for the severe systemic genotoxicity displayedby Atm^(−/−) mice, the immune response at each point of blood collectionwas characterized and compared to wildtype mice. Though the innateresponse primarily drives DSS-colitis and potentially the observedgenotoxicity, we hypothesized the adaptive immune response would be alsomodulated and play a role in driving genotoxicity. Transcript levels ofTh1, Th17/23, and Th2 cytokines in the peripheral blood, wheregenotoxicity was measured, were quantified via quantitative real-timePCR (FIG. 11). Atm^(−/−) mice displayed greater upregulation of TNF-α(Tnf1) and MCP-1 (Ccl2) during the second remission period and after thethird cycle of treatment (p<0.05) than wildtype mice, indicative of achronically activated innate immune response. Levels of IL-6, IL-12, andIL-23 were also significantly upregulated in Atm^(−/−) compared towildtype mice after treatment cycles and during remission periods,indicative of T-cell mediated proinflammatory responses. Interestingly,IL-17 transcripts were not detected in both genotypes. Similarly, lowerlevels of IL-17, and increased levels of Th12/23 and Th1 cytokines havebeen previously observed in DSS treated C57BL/6 mice (29).

Although levels of IFN-γ (Ifng), also an indicator of a T-cell response,were modulated in Atm^(−/−) mice, no significant differences were seencompared to wildtype mice. The Th2 response was more pronounced inAtm^(−/−) mice in chronic phases of treatment, characterized byincreased expression of IL-4 (II4), IL-10 (II10), and TGF-β (Tgfb). Adefect in tolerance mechanisms associated with anti-inflammatorycytokines are therefore most likely not the cause of increasedsensitivity of Atm^(−/−) mice to chronic inflammation.

T-cell populations in the peripheral blood were also characterized byflow cytometry for CD4, CD8α, CD69, an early activation marker of allT-cells including NK-cells (30), and CD44, expressed on leukocytes andinvolved in recruitment, activation, and effector functions (31) (FIGS.12A-D). Spontaneously, Atm^(−/−) mice have significantly lower counts ofmature CD4⁺ T-cells than wildtype and heterozygous mice, in agreementwith previous findings (FIG. 12C) (32-34). However, a significantlylarger proportion of these T-cells are activated in response to DSStreatment compared to wildtype mice as shown by positive staining forCD69 and CD44 (FIGS. 12A and 12B). Heterozygous mice demonstratedsimilar levels of positive staining compared to wildtype mice (FIG.12D). Numbers of CD4 and CD8α positive T-cells were also significantlymodulated throughout treatment, most likely representing the dynamicinflux and efflux of cells between the site of inflammation and theperipheral blood. Percent activated T-cells remained significantlyelevated especially in remission periods in Atm^(−/−) compared towildtype mice until the end of the study, indicating a persistent immuneresponse.

Discussion

Atm^(−/−) mice have decreased numbers of circulating T-cells due tointrinsic defects in T-cell progenitors and consequential developmentalabnormalities of single positive thymocytes (9, 32). However, thoughlower in number, mature T-cells from A-T patients have been shown to befunctionally normal; demonstrating the capability of mounting acompetent immune response (35). Atm^(−/−) mice also do not developspontaneous colitis or other inflammatory disorders of thegastrointestinal tract (36). However, when challenged with DSS causing adisruption in the integrity of the intestinal epithelial barrier, wedemonstrated that Atm^(−/−) mice exhibit greater severity of clinicalsymptoms and mortality rates, DNA damage to peripheral leukocytes anderythroblasts, and mount an even stronger immune response characterizedby inflammatory cytokines and circulating activated T-cells compared towildtype mice. A significant gene dosage effect was not seen in terms ofdisease activity or percent activated T-cells, though a small increasein genotoxicity over wildtype mice was seen after the third cycle;indicating potential compensatory mechanisms for heterozygosity of Atm.Similarly, Atm heterozygosity does not increase tumor susceptibility inmice after γ-irradiation compared to wildtype mice (37), thoughincreased susceptibility to mammary tumorigenesis is seen in a Brca1mutant background, compared to Atm sufficient mice (38).

The observed systemic DNA damage can be assumed to be inflammationmediated since DSS itself is not directly genotoxic (39, 40). Reactivespecies derived from inflammatory cells through oxidative burst maycause oxidative and nitrative damage both locally and systemicallymeasured by 8-oxoguanine and nitrotyrosine formation. Localization ofthis damage to the villi, surrounding epithelial cells, and infiltratinginflammatory cells may be due to DSS-induced villous atrophy andextensive epithelial turnover. Though ATM does not manifest a protectiverole in terms of protein damage, 8-oxoguanine levels were found to behigher in Atm^(−/−) mice, demonstrating lack of repair of oxidative DNAdamage in addition to strand breaks. Interestingly, although DNA damageremained elevated, clinical symptoms of colitis were not present duringremission periods and after the end of treatment, emphasizing the roleof sub-clinical inflammation in the induction of DNA damage and the lackof repair of previously incurred damage. High levels ofinflammation-associated oxidative stress, in addition to inherentdeficiencies in repair of the resultant DNA damage, and partialsuppression of DNA damage response-dependent apoptosis (41, 42) mayexplain the extreme sensitivity of the Atm^(−/−) mice. An accumulationof DNA damage over the entire treatment period amidst slow DNA repairand cell turnover is therefore a probable explanation for increasinglevels of DNA damage in Atm^(−/−) mice, taking into account therelatively long lifespan of lymphocytes. Differentiation of naïve Tcells into Th1 and Th17 effector cells could cause proliferation (43),in which accumulated DNA damage can lead to fixation of mutations.

Accumulation of double strand breaks can lead to chromosome breaks andmicronuclei formation (44). Damage to erythroblasts in the bone marrowmay be a humoral effect of inflammation-associated DNA damage, as withthe peripheral leukocytes. Pro-inflammatory cytokines are preferentiallyreleased by cells that have migrated to the sites of inflammation ratherthan by resident macrophages (4). A recirculating pool of activatedmonocytes may recruit and activate effector cells, coming into contactwith erythroblasts in the bone marrow, causing the observedclastogenicity.

The persistently activated immune response mounted by Atm^(−/−) micedemonstrate a possible role of ATM in immunoregulation during DSStreatment. The recruitment of myeloid-derived cells to the site ofinflammation, along with resident dendritic cells, allow forphagocytosis of DSS particles and activation of the adaptive responseinvolving differentiation of naïve T-cells into activated effector cells(45). The prolonged presence of a larger percentage of activated T-cellsin Atm^(−/−) mice, which harbor much lower total counts of CD4⁺ T cells,represents the capacity of these mice to mount a successful yet damagingimmune response despite this deficiency. An increase in messenger levelsof inflammatory cytokines especially during remission periods is initself evidence for systemic distribution, which also corresponded tolevels of activated T-cells and genotoxicity in the peripheral blood.This persistent activation of T-cells and upregulation of cytokines canresult in increased activity of macrophages and oxidative bursts, whichmay be a potential explanation for the observed direct genotoxicity toperipheral leukocytes. Further mechanisms may be investigated byadministration of enzymatic inhibitors or anti-proliferative agents.

Recent evidence has pointed to the role of DNA damage response involvingATM in modulating an immune response. Genotoxic insult and activation ofthe ATM/ATR pathway was shown to upregulate ligands for the NKG2Dreceptor in mice and in humans, present on all NK cells, γδ-T cells, andactivated CD8⁺ T cells (46). This serves as a link between genotoxicstress and immune activation. Therefore, not only can the immuneresponse potentially cause DNA damage via oxidative burst, but DNAdamage itself can further activate NK-cells, potentially causing furtherdamage if not properly repaired, as in Atm^(−/−) mice. Nuclear ATM hasalso been shown to directly bind NF-κB essential modulator (NEMO), amodulator of NF-κB, leading to cytoplasmic translocation and activationof NF-κB, resulting in transcription of inflammatory and prosurvivalresponse genes specifically in response to tolerable DNA damage (47).These varying modes of activation signify a coupling of stress responseand cell survival.

The lack of ATM in these aspects could result in abnormal signaling interms of response to genotoxic stress in the setting of chronicinflammation. Transcriptional repression of ATM has recently been foundselectively in naïve T-cells of rheumatoid arthritis patients, in whichthere is increased DNA damage thought to be independent of inflammation;indicating alternative modes of increased DNA damage in cells deficientin ATM (48). Aside from ATM deficiency, FEN1 deficiency, amultifunctional endonuclease, leads to incomplete digestion of DNA inapoptotic cells and results in chronic inflammation and autoimmunity(49). Similarly, increased levels of DNA damage resultant from chronicinflammation, due to an inherent deficiency in double strand breakrepair in Atm^(−/−) mice, may actually further promote inflammation andcause further DNA damage in a positive feedback loop. ATM may playtherefore a protective role, not only as a DNA damage sensor, but alsoas an immunoregulator. The increased sensitivity to DSS treatment wasnot only present as clinical symptoms from localized inflammation in thecolon, but manifested itself as a systemic insult characterized bygenotoxicity and activation of immune responses.

In summary, Atm^(−/−) mice are more sensitive to DSS-induced acute andchronic inflammation than heterozygous or wildtype mice, especiallyduring remission and up to four weeks after the final round oftreatment, demonstrating lack of repair of incurred damage. Increasedsensitivity was characterized by higher incidence of mortality, clinicalsymptoms, systemic genotoxicity to peripheral leukocytes anderythroblasts, and an activated immune response including increasedtranscripts of inflammatory cytokines in the peripheral blood. Systemicgenotoxic stress induced by byproducts of inflammation may be able tofurther promote inflammatory responses and pro-survival mechanisms, viathe intricate involvement of ATM. The lack of this protein causesfurther DNA damage and genetic instability, along with a more potentimmune response, possibly due to other pathways alerting and furtheractivating the immune response, or by defects in resolution of activatedeffector cells. ATM therefore can be inferred to play a role inimmunoregulation and maintenance of genetic stability duringinflammation, and be considered as a potential target for not onlychronic inflammatory diseases but also for cancer therapy andprevention.

REFERENCES CITED IN EXAMPLE 2

-   1. See Example 1.-   2. Coussens L M, Werb Z. Inflammation and cancer. Nature 2002; 420:    860-7.-   3. Eaden J A, et al. Gut 2001; 48: 526-35.-   4. Sartor R B. et al. Nat Clin Pract Gastroenterol Hepatol 2006; 3:    390-407.-   5. Bredemeyer A L, et al. Nature 2006; 442: 466-70.-   6. Callén E, et al. Cell 2007; 130: 63-75.-   7. Lavin M F, Shiloh Y. Annu Rev Immunol 1997; 15: 177-202.-   8. Lavin M F. Nat Rev Mol Cell Biol 2008; 9: 759-69.-   9. Bagley J, et al. Blood 2004; 104: 572-8.-   10. Lumsden J M, et al. J Exp Med 2004; 200: 1111-21.-   11. Meira L B, et al. J Clin Invest 2008; 118: 2516-25.-   12. Hofseth L J, et al. Proc Natl Acad Sci 2003; 100: 143-8.-   13. Okayasu I, et al. Gastroenterology 1990; 98: 694-702.-   14. Dieleman L A, et al. Gastroenterology 1994; 107: 1643-52.-   15. Tardieu D, et al. Cancer Lett 1998; 134: 1-5.-   16. Liao J, et al. Mol Carcinog 2008; 47: 638-46.-   17. Kohonen-Corish M R J, et al. Cancer Res 2002; 62: 2092-7.-   18. Reliene R, et al. DNA Repair 2006; 5: 852-9.-   19. Murthy S N, et al. Dig Dis Sci 1993; 38: 1722-34.-   20. Olive P L, et al. Nat Protocols 2006; 1: 23-9.-   21. Goldstine J V, et al. DNA Repair 2006; 5: 432-43.-   22. Muslimovic A, et al. Nat Protocols 2008; 3: 1187-93.-   23. Abramoff M, et al. J Biophotonics Int 2004; 11: 36-42.-   24. Lossos I S, et al. Leukemia; 17: 789-95.-   25. R Development Core Team. R: a language and environment for    statistical computing. Vienna (Austria): R Foundation for    Statistical Computing; 2007. ISBN 3-900051-07-0.-   26. Barzilai A, et al. DNA Repair 2002; 1: 3-25.-   27. Pinlaor S, et al. Carcinogenesis 2004; 25: 1535-42.-   28. Liu J S, et al. Am J Pathol 2001; 158: 2057-66.-   29. Melgar S, et al. Am J Physiol Gastrointest Liver Physiol 2005;    288:G1328-38.-   30. Testi R, et al. Immunol Today 1994; 15: 479-83.-   31. Puré E, Cuff C A. Trends Mol Med 2001; 7:213-21.-   32. Vacchio M, et al. Proc Natl Acad Sci 2007; 104: 6323-8.-   33. Paganelli R, et al. J Clin Immunol 1992; 12: 84-91.-   34. Xu Y, et al. Genes Dev 1996; 10: 2411-22.-   35. Giovannetti A, et al. Blood 2002; 100: 4082-9.-   36. Barlow C, et al. Cell 1996; 86: 159-71.-   37. Mao J H, et al. Oncogene 2008; 27:6596-600.-   38. Bowen T J, et al. Cancer Res 2005; 65:8736-46.-   39. Mori H, et al. Nutr Cancer 1984; 6: 92-7.-   40. Nagoya T, et al. Pharmacometrics 1981; 22: 621-7.-   41. Pusapati R, et al. Proc Natl Acad Sci 2006; 103: 1446-51.-   42. Westphal C, et al. Nat Genetics 1997; 16: 397-401.-   43. Sprent J, Tough D F. Science 1994; 265: 1395-400.-   44. Obe G, et al. Mutat Res 2002; 504: 17-36.-   45. Dieleman L A, et al. Clin Exp Immunol 1998; 114: 385-91.-   46. Gasser S, et al. Nature 2005; 436: 1186-90.-   47. Wu Z H, et al. Science 2006; 311: 1141-6.-   48. Shao L, et al. J Exp Med 2009; 206: 1435-49.-   49. Zheng L, et al. Nat Med 2007; 13: 812-9.

Example 3: Additional Data on Characterization of Systemic Genotoxicityand the Potential Mechanisms Involved

In an effort to further characterize susceptible cell types to DNAdamage, subpopulations of leukocytes in the peripheral blood as well ascells from distant lymphoid and non-lymphoid tissues were analyzed forDNA single- and double-stranded breaks. We also hypothesized thatmediators of inflammation such as tumor necrosis factor-alpha (TNF-α)would be sufficient and necessary to induce the observed systemicgenotoxicity in mice without preexisting inflammation. DNA damage wasfound in both lymphoid and non-lymphoid cell types, manifesting moredamage to CD4 and CD8 T-cells versus other cell types. TNF-α wassufficient to induce systemic genotoxicity in wildtype mice. Examinationof transcript levels as well as protein expression levels of the DNAdouble strand break recognition and repair protein ataxia telangiectasiamutated (ATM) in CD4 and CD8 T-cells revealed no differences in theIL-10^(−/−) compared to wildtype mice.

Methods

Animals.

Gαi2^(−/−) (B6/129Sv background, 3 months) (2) IL-10^(−/−) (C3H/HeJBirbackground, 3 or 6 months) mice were housed in the UCLA Department ofLaboratory and Animal Medicine under specific pathogen free conditions,autoclaved bedding and food, with standard rodent chow diet, acidifieddrinking water, and 12:12 light:dark cycle. All mice were bred at UCLAexcept IL-10^(−/−) and C3H/HeJ which were purchased from JacksonLaboratory (Bar Harbor, Me.).

Blood/Tissue Collection.

Peripheral blood was collected via the facial/mandibular vein with a 5mm lancet (Braintree Scientific, Braintree, Mass.) into EDTA coatedcollection tubes (Braintree Scientific). For magnetic bead separations,a terminal bleed utilizing 500 μL was used. For the comet assay, bloodwas immediately diluted 1:1 in RPMI/10% DMSO and immediately frozen at−80° C. until further analysis. Freshly collected blood was immediatelyprocessed for all other assays. Spleens, peripheral lymph nodes (PLN)including both axillary and inguinal lymph nodes (at least 5/mouse) andmesenteric lymph nodes (MLN) (at least 5/mouse) were harvested andprocessed into single cell suspensions in RPMI/10% FBS for furtheranalysis. Isolation of intestinal epithelial/intraepithelial cells wasdone as described previously (3).

Assessment of DNA Damage

Alkaline Comet Assay.

To detect DNA strand breaks, as well as alkali labile sites in DNA, thealkaline comet assay was performed as described elsewhere (4). Frozenblood or single cell suspensions were thawed on ice and further diluted1:15 in PBS before further sample preparation. After lysis andelectrophoresis, gels were stained with SYBR Gold (Molecular Probes) andvisualized under a fluorescent microscope (Olympus Ax70, Tokyo, Japan)at 10× magnification. Comet images were captured and analyzed with theCASP image analysis program (http://casp.sourceforge.net). The olivetail moment, which represents both tail length and fraction of DNA inthe tail, was used for data collection and analysis, in which apoptoticcells were excluded under previously proposed criteria (4).

Determination of Oxidative DNA Damage.

For determination of oxidative DNA damage the enzyme hOgg1-modifiedcomet assay was used (5). After lysis in the alkaline comet assay,samples were washed in an enzyme wash buffer (40 mM HEPES, 0.1M KCl, 0.5mM EDTA, 0.2 mg/ml BSA, pH 8.0) then incubated at 37° C. for 10 min ineither control (buffer with no hOGG1) or enzyme treated (buffer withhOGG1) solutions according to the manufacturer's recommendations (NewEngland Biolabs, Ipswich, Mass.). Both control and enzyme treated gelswere then placed in electrophoresis buffer and processed identically tothe alkaline comet assay.

Immunofluorescence.

Peripheral blood and splenocytes were incubated in Buffer EL (Qiagen,Valencia, Calif.) on ice to remove erythrocytes. Other single cellsuspensions did not require erythrocyte lysis. Samples were thenprocessed on coverslips as described elsewhere (6). Briefly, afterpermeabilization and blocking, cells were incubated with mouseanti-phospho-Histone H2A.X S139(P) (Upstate, Temecula, Calif.) at 1:400followed by FITC-conjugated anti-mouse IgG (Jackson ImmunoResearch, WestGrove, Pa.) at 1:200. Coverslips were mounted with VECTASHIELD with4,6-diamidino-2-phenylindole (Vector Laboratories, Burlingame, Calif.).Images were captured with FISH analysis software (CytoVision, AppliedImaging Corporation, San Jose, Calif.) connected to a Zeiss automatedFISH microscope. At least 125 cells were counted and cells with morethan four distinct foci in the nucleus were considered positive (6).Apoptotic cells are easily distinguishable due to presence of 10-foldhigher number of nuclear foci than highly damaged cells (7), and werenot included in analyses.

In Vivo Micronucleus Assay.

Micronucleus formation was determined in normochromatic erythrocytes asmicronucleated normochromatic erythrocytes per 1000 normochromaticerythrocytes as described previously (1, 8).

Magnetic Bead Isolation of Cells.

Individual subpopulations of cells in the peripheral blood were isolatedby magnetic bead isolation. Leukocytes were separated from whole bloodby density centrifugation with Histopaque-1119 (Sigma) according tomanufacturer's instructions. Cells were then labeled with MicroBeadsconjugated to monoclonal mouse antibodies (anti-CD4, anti-CD8,anti-CD19, anti-CD11c, or anti-CD3) and magnetically separated bypositive selection on MS columns (Miltenyi Biotec, Bergisch Gladbach,Germany).

Injection of Cytokines.

Mouse TNF-α (Sigma) and/or mouse IL-1β (Sigma) were injected via thetail vein at 500 ng/mouse and 100 ng/mouse, respectively, dissolved insaline. Control animals received vehicle only. Peripheral blood wascollected at 1 hr, 2 hrs, 4 hrs, and 24 hrs after injection forgenotoxicity assays.

Gene and Protein Expression.

Gene expression was measured as mRNA transcript levels of ataxiatelangiectasia mutated (ATM) and xeroderma pigmentosum group C(XPC)standardized to TATA box binding protein (TBP), the internal controlgene in peripheral leukocytes by quantitative real time PCR aspreviously described (Westbrook et al) utilizing Taqman Gene Expressionkits for ATM and TBP (ABI). Protein expression was measured as meanfluorescence intensity of anti-ATM protein kinase (pSer1981) by flowcytometry. Briefly, cells were stained for cell surface markers(PE-anti-CD4 or PerCP anti-CD8), and then processed for intracellularstaining. Cells were fixed with 1.5% paraformaldehyde for 10 min at roomtemperature, permeabilized, and then stained with FITC-anti-pATM(Rockland Immunochecmicals, Inc) or the appropriate isotype control.

Statistical Analyses.

Results are expressed as mean±standard error of the mean. Statisticalsignificance was determined by nonparametric one-way/two-way ANOVAs withDunn's multiple comparison post test or paired Student's t-tests,defined as p<0.05. Calculations were performed with the statisticalanalysis software Graph Pad Instat version 3.00 (Graph Pad Software, SanDiego, Calif.) or R: A language and environment for statisticalcomputing. (R Development Core Team (2007). R foundation for StatisticalComputing, Vienna, Austria. ISBN 3-900051-07-0, URLhttp://www.R-project.org).

Results

Differences in Susceptibility to DNA Damage in Peripheral BloodSubpopulations.

In order to determine leukocytes that may be more or less sensitive toinflammation-associated genotoxicity, subpopulations in the peripheralblood were isolated via magnetic bead separation and analyzed for DNAdamage in Gαi2^(−/−) and IL-10^(−/−) mice. CD4⁺ T-cells from IL-10^(−/−)mice had significantly more DNA strand breaks as measured by the meanolive tail moment in the comet assay and as percent positive cells forγ-H2AX foci compared to wildtype littermates and to other cell typesincluding CD19⁺ B-cells and CD11b⁺ macrophages (FIGS. 13A and 13B). Theeluate, which contained cell types not positively selected for bymagnetic beads, from IL-10^(−/−) mice seemed to contain significantlyhigher percent positive cells for γ-H2AX foci compared to wildtype mice.

In Gαi2^(−/−) mice, whose disease progression is faster and more severethan in IL-10^(−/−) mice, DNA strand breaks were observed morefrequently in multiple cell types including CD4⁺ and CD8⁺ T-cells, aswell as in CD11b⁺ macrophages compared to heterozygous littermates whichdo not develop colitis and to CD19⁺ B-cells and cells in the eluate(FIGS. 13C and 13D). Results from the alkaline comet assay and γ-H2AXimmunostaining correlated with each other, demonstrating a wider arrayof cell types damaged in the peripheral blood compared to theIL-10^(−/−) mice. Clinical severity of inflammation therefore maycorrelate to a wider array of cell types affected.

Genotoxicity in Lymphoid Organs

Lymphoid organs such as the spleen, mesenteric lymph nodes, andperipheral lymph nodes were isolated into single cell suspensions fromIL-10^(−/−) and wildtype mice, and analyzed for DNA damage.Surprisingly, all lymphoid tissues demonstrated significant genotoxicitycompared to wildtype mice, characterized by DNA single- anddouble-stranded breaks, comparable to that seen in the peripheralleukocytes (FIGS. 14A-14C). Mesenteric lymph nodes, though physically inclosest contact with the site of inflammation in the colon, demonstratedsimilar levels of DNA damage found in the peripheral lymph nodes,collected at distant sites relative to the site of inflammation. Thespleen also showed similar levels of strand breaks, indicating systemiccirculation of the components and cell types in the immune responseinvolved in potentially causing the observed genotoxicity.

Previously, we have demonstrated DNA damage to correlate to diseaseactivity in the peripheral blood of IL-10^(−/−) mice (1). Similarly,utilizing younger IL-10^(−/−) mice of 8 weeks of age with subclinicalinflammation demonstrating lower clinical disease activity indices thanthose at 6 months of age, DNA damage in all the lymphoid organs wasfound to be lower compared to the older mice (FIGS. 14A-14C). Levels ofoxidative base damage, measured by the alkaline comet assay with hOgg1incubation, however were similar in the 8 week old mice compared to the6 month old mice (FIG. 14C). Therefore, systemic DNA damage in the formof strand breaks correlates to disease activity in both the peripheralblood as previously demonstrated and the lymphoid organs of these mice.

Large and Small Intestinal Epithelial Cell Genotoxicity

In addition to peripheral leukocytes and lymphoid organs, intestinalepithelial cells and intraepithelial cells were isolated from the largeand small intestine of IL-10^(−/−) (6 months of age) and wildtype mice.As expected from the sites of inflammatory activity, epithelial cellsfrom the large intestine harbored greater genotoxicity than those fromthe small intestine, and IL-10^(−/−) mice demonstrated greatergenotoxicity to intestinal epithelial cells of both the small intestineand large intestine than wildtype mice (FIGS. 15A and 15B). Genotoxicitywas characterized by presence of DNA single- and double-stranded breakswith oxidative base damage.

TNF-α is Sufficient to Induce DNA Damage

In order to determine sufficiency of a cytokine in inducing DNA damage,recombinant mouse TNF-α or saline was injected into the tail vein ofwildtype mice (6-8 weeks of age) without any basal inflammatoryactivity. As soon as 1 hour post-injection, DNA damage to peripheralleukocytes was observed only in treated mice, which continued to remainelevated until approximately 4 hours post-injection, and then appearedto be repaired within 24 hours post-injection (FIGS. 16A and 16B).Damage was observed in both the alkaline comet assay and by formation ofγ-H2AX foci. Micronuclei formation to erythroblasts measured incirculating normochromatic erythrocytes and indicative ofclastogenicity, was minimally yet significantly elevated 48 hourspost-injection compared to before injection (FIG. 16C).

In addition to the peripheral leukocytes, similar profiles of DNA damagewere observed in the lymphoid organs such as in the spleen, mesentericand peripheral lymph nodes 1.5 hours post-injection of the identicaldose of recombinant TNF-α (FIGS. 17A-D). DNA strand breaks were onceagain most evident in CD4 and CD8 T-cells versus other cell types in theperipheral blood, as well as in the spleen and the peripheral lymphnodes. DNA damage was evident in the form of both single and doublestrand breaks accompanied by oxidative base damage as demonstrated bythe mean olive tail moments and percent positive cells for γ-H2AX foci.

To determine whether or not a combinatorial administration of cytokineswould yield a different genotoxicity profile than with TNF-α alone toperipheral leukocytes, recombinant mouse IL-β was injected via the tailvein at 100 ng per mouse alone or in combination with 500 ng ofrecombinant mouse TNF-α. Administration of IL-β alone resulted inmaximum DNA damage to peripheral leukocytes occurring at 4 hourspost-injection (versus 1 hour post-injection for TNF-α alone), followedby complete repair of damage by 24 hours post-injection (FIGS. 18A-C).However, when both cytokines were administered together, strand breaksand oxidative base damage measured by the alkaline comet assay increaseddramatically at 4 hours post-injection and remained elevated even after24 hours post-injection (FIG. 18A). DNA double strand breaks,specifically measured by γ-H2AX foci formation, however increased assoon as 1 hour post-injection, and then remained at the same levelsuntil 24 hours post-injection indicating lack of DNA repair (FIG. 18B).Micronuclei formation was also elevated at 48 hours post-injection (FIG.18C), indicating clastogenicity.

Increased Genotoxicity in IL-10−/− Mice is not Due to DecreasedExpression of ATM

A recent study demonstrated that CD4 T-cells from rheumatoid arthritispatients selectively were deficient in transcript and protein levels ofATM, causing increased DNA strand breaks and rendering T-cells sensitiveto apoptosis and premature immunosenescence (9). Levels of expression interms of transcript levels and protein levels of ATM were thereforeanalyzed in order to see whether or not similar decreased DNA repaircapabilities were a potential explanation for sustained systemicgenotoxicity in the peripheral leukocytes of IL-10 mice with colitis.Transcript levels of ATM were almost identical in wildtype mice andIL-10 KO mice, as well as protein expression of activated pATM measuredby flow cytometry (FIG. 19).

Discussion

Further characterization of intestinal inflammation-associated systemicgenotoxicity as well as the determination of underlying mechanisms willgive insight into the progression of associated diseases arising outsidethe intestinal tract such as lymphomas, effects on lymphocyte mediatedimmune responses, as well as illuminate potential areas of therapeuticutility. In addition to that of intestinal inflammation, mechanisticinsights will carry much broader implications as patients with variousother inflammatory diseases have recently been found to carry DNA damageto peripheral leukocytes or to specific subpopulations thereof. Theseinclude type 1 and 2 diabetes (10), rheumatoid arthritis (9), systemiclupus erythromatosus (11), liver cirrhosis (12), and pre-neoplasticconditions such as myelodysplastic syndrome (13).

DNA damage to CD4 and CD8 T-cells predominantly versus other cell typesin the peripheral blood in IL-10^(−/−) mice demonstrates thatinflammation-induced DNA damage is not completely random, given thatT-cells only represent 30-40% of total circulating leukocytes. In themore severe Gαi2^(−/−) model, though the DNA of CD4 and CD8 T-cells mayhave been damaged first due their relative sensitivity, other cell typesincluding the macrophages and to a lesser extent, B-cells were alsodamaged. This may indicate a correlation between severity of pathologyand the inflammatory response with DNA damage to multiple cell types. Inaccordance with our data, others have also found relatively more damageto T-cells versus other cell types in the blood, such as in rheumatoidarthritis patients (9), and both basally and after treatment withhydrogen peroxide in isolated peripheral blood (14). Further basaldifferences have also been observed between naïve and memory T-cells inwhich the latter has been found to have greater DNA damage and thus ashorter lifespan than the naïve T-cells, which have a half life of150-160 days (15). Longer lifespan, however could also lead toaccumulation of DNA damage over time, despite having intact DNA repaircapabilities, such as when comparing generally long-lived T-cells toshort-lived B-cells, which depends on many factors including antigenicstimulation (14). The sensitivity of the CD4 and CD8 T-cell populationsduring inflammation may indicate excessive cellular stress, in whichrepair and cellular defense mechanisms cannot keep up with the oxidativeenvironment of an inflammatory response. This can be supported by thefact that activated T-cells or T-cells infected with humanimmunodeficiency virus (HIV) contain elevated levels of mitochondrialsuperoxide and thus carry a reduction in the mitochondrial membranepotential (16). Other cell types, such as macrophages are selectivelyknown to have defense mechanisms such as the constitutive expression ofheme-oxygenase 1 (HO-1) to act as an “anti-inflammatory” agent which isfurther upregulated during acute inflammation by production of carbonmonoxide and bilirubin (17), as well as a large number of strongantioxidant enzymes including superoxide dismutases, catalases, andglutathione peroxidases. Therefore, differing ROS scavenging and levelsof antioxidant response enzymes, DNA repair capabilities, life span, andcellular permeability may explain the differences observed insensitivity of cell types and in the context of the clinical severity ofdisease.

Genotoxicity to the lymphoid organs including the mesenteric lymphnodes, peripheral lymph nodes, and spleen, as well as to the intestinalepithelial cells in the IL-10^(−/−) mice indicate both local as well assystemic damage that either may be indicative of circulating damagedleukocytes into and out of the peripheral lymphoid organs, or leukocytesthat are damaged at these distant sites due to a systemic inflammatoryresponse. Importantly, IL-10^(−/−) mice demonstrate a correlation of DNAdamage to severity of disease activity (which progresses with age) inthe peripheral lymphoid organs. This disease activity correlation haspreviously been demonstrated in the peripheral leukocytes ofchemically-induced colitis as well as in the IL-10^(−/−) mice (1).

It is important to note that many models of intestinal inflammationincluding Gαi2^(−/−), IL-10^(−/−), and DSS-treated mice display systemicinflammation characterized by presence of activated T-cells andincreased cytokine production such as TNF-α and IFN-γ, in not only thecolon and lamina propria, but also in splenocytes and peripheral lymphnodes (18-20). Systemic inflammatory activation and immunehyper-responsiveness in these models observed in distant immune cellsmay therefore serve as a mechanism for the observed systemicgenotoxicity.

We have found that a single injection of recombinant mouse TNF-α issufficient to induce genotoxicity to peripheral leukocytes in healthywildtype mice. Treatment for Crohn's disease as well as ulcerativecolitis currently involves TNF-α blockers such as Remicade®, indicatingthe direct role of TNF-α in pathogenesis. It still remains to beexplored whether or not the ligand binding to the TNF receptors itself,or downstream pathways involved in inflammatory activation of immunecells are responsible for the observed DNA damage. Interestingly,similar to what was seen in the models of chronic intestinalinflammation, CD4 and CD8 T-cells proved to be more sensitive than othercell types in the peripheral blood, and the peripheral lymphoid organsalso manifested genotoxicity, albeit less than observed in the geneticmodels of colitis. High bioavailability of TNF-α in the peripherallymphoid tissues may contribute to the observed DNA damage to thesesites, since only a single bolus dose was administered. When combinedwith injection of IL-1β, another prominent cytokine found to be elevatedin multiple models of chronic intestinal inflammation, DNA damagepersisted for up to 24 hours without repair, indicating synergistic ordelayed effects in the induction of genotoxicity. Circulating cytokinessuch as TNF-α and IL-1β in chronic intestinal inflammation thereforeplay a role in inducing systemic genotoxicity even without basalinflammatory activity. Further DNA damage, when persistent, may lead togenetic alterations which would be sufficient to create an inflammatorymicroenvironment, even if no previous inflammatory state is observed(21). The persistently elevated levels of large networks ofcytokines/chemokines as well as their interactions, which betterrepresent actual active intestinal inflammation, may therefore explainthe chronically elevated levels of DNA damage observed systemically inmultiple cell types.

In rheumatoid arthritis patients, expression of ATM, and DNA doublestrand break recognition and repair protein, was found to bedownregulated selectively in CD4 T-cells explaining their susceptibilityto increased DNA damage and higher turnover rates (9), and we haverecently demonstrated increased susceptibility to chemically inducedcolitis in ATM deficient mice (8). Therefore, the DNA repair capabilityof leukocytes in terms of expression of ATM and XPC, a nucleotideexcision repair protein, was analyzed in IL-10^(−/−) mice with colitis.Transcript levels of ATM and XPC were identical to wildtype mice, andprotein levels of pATM were also not significantly different in CD4 orCD8 T-cells between the two genotypes, indicating competent DNA repaircapabilities. Other models such as the Gαi2^(−/−) mice whosepathogenesis involves different mechanisms, may however show differentDNA repair capabilities compared to wildtype mice.

In summary, the use of DNA damage assays to diagnose and monitorpatients in chronic intestinal inflammation is feasible due to thestrong correlation to disease activity in mouse models, and preliminarypilot data obtained from blood samples of IBD patients with or withoutactive disease (see Example 4, below). Mechanisms and furtherimplications of systemic genotoxicity are still being investigated,though susceptible cell types have been identified and cytokines such asTNF-α and IL-1β have been found to be sufficient to induce DNA damage.Further work is necessary to outline sufficiency and necessity of eventsdownstream of cytokine administration such as with TNFR deficient miceor administration of enzymatic inhibitors and anti-proliferative agents.

REFERENCES CITED IN EXAMPLE 3

-   1. Westbrook A M, et al. Cancer Res 2009; 69(11):4827-34.-   2. Rudolph U, et al. Nat Genet. 1995; 10(2):143-50.-   3. Van der Heijden P J, Stok W. Journal Immunol Methods 1987;    103(2):161.-   4. Olive P L, et al. Nat Protocols 2006; 1(1):23-9.-   5. Smith C C, et al. Mutagenesis 2006; 21(3):185-90.-   6. Goldstine J V, et al. DNA Repair 2006; 5(4):432-43.-   7. Muslimovic A, et al. Nature Protocols 2008; 3(7):1187.-   8. Westbrook A M, et al. Cancer Research 2010; 70(5):1875-84.-   9. Shao L, et al. J Exp Med 2009; 206(6):1435-49.-   10. Pitozzi V, et al. Mutation Research/Fundamental and Molecular    Mechanisms of Mutagenesis 2003; 529(1-2):129-33.-   11. McConnell J R, et al. Clinical and experimental rheumatology;    20(5):653.-   12. Grossi S, et al. European Journal of Gastroenterology &    Hepatology 2008; 20(1):22-5 10.1097/MEG.0b013e3282f163fe.-   13. Watson D, et al. Leukemia Research 2009; 33(Supplement    1):595-56.-   14. Weng H, et al. Mutation Research/Genetic Toxicology and    Environmental Mutagenesis 2008; 652(1):46-53.-   15. Scarpaci S, et al. Mechanisms of ageing and development 2003;    124(4):517-24.-   16. Castedo M, et al. European Journal of Immunology 1995;    25(12):3277-84.-   17. Yachie A, et al. Experimental Biology and Medicine 2003;    228(5):550-6.-   18. Dieleman L A, et al. Clinical and Experimental Immunology 1998;    114(3):385.-   19. Rennick D M, et al. J Leukoc Biol 1997; 61(4):389-96.-   20. Huang T T, et al. Int Immunol 2003; 15(11):1359-67.-   21. Mantovani A, et al. Cancer-related inflammation. Nature 2008;    454(7203):436-44.

Example 4: Peripheral Leukocytes from IBD Patients DemonstrateGenotoxicity

This example demonstrates presence of DNA damage, as detected via thealkaline comet assay and γ-H2AX foci formation, in an analysis ofperipheral leukocytes of 19 inflammatory bowel disease (IBD) patientswith active disease and in those in remission.

A pilot study utilizing 19 IBD patients from Mount Sinai Medical Centerdemonstrated significant genotoxicity to peripheral leukocytes in boththe alkaline comet assay and in γ-H2AX foci formation. Patients withactive disease as well as those in remission were analyzed (FIG. 20).Active Crohn's disease patients demonstrated severe DNA damage by bothassays, while those in remission were relatively negative for DNAdamage. A couple patients with other diseases including combinedvariable immunodeficiency disease and hypogammaglobulinemia demonstratedDNA damage as well. Further studies with more negative controls can bedone for further validation.

Total Number of Positive for Disease Patients DNA damage Active Crohn'sdisease 2 2 Remission Crohn's disease 6 2 Common variable 7 2immunodeficiency Ulcerative colitis 2 1 Hypogammaglobulinemia 1 0

Example 5: Systemic Genotoxicity in Peripheral Blood in a Mouse Model ofAsthma

This example demonstrates that IL-13 overexpression in mouse lungs, ananimal model for asthma, triggers systemic genotoxicity that can bedetected in peripheral blood. The results presented in this exampledemonstrate that IL-13 is associated with a systemic induction ofgenotoxic parameters such as oxidative DNA damage, single and double DNAstrand breaks, micronucleus formation, and protein nitration. Theinflammation induced genotoxicity found in asthma extends beyond theprimary site of the lung to circulating leukocytes and erythroblasts inthe bone marrow, eliciting systemic effects. Thus, markers ofgenotoxicity detected in peripheral blood serve as markers for detectionand monitoring of asthma.

We used a genetically modified mouse model originally developed by theElias lab (Ooi 2010) which allow for tetracycline activated conditionalover-expression of IL-13 in the Clara Cells of the lungs. We thencollected peripheral blood from these asthmatic mice and performedgenotoxic assays throughout the progression of the disease.

Materials. & Methods:

Transgenic Mice.

The CC10-rtTA-IL13 transgenic (TG) mouse is a well-characterized modelof asthma (Zheng 2000). Clara cell 10-kDa (CC10) gene promoter is usedfor conditionally expression of IL13 in the mouse lung inducible bydoxycycline. CC10-rtTA-IL13 transgenic (TG) mice were generated in Dr.Talel Chatila's lab at the David Geffen School of Medicine University ofCalifornia Los Angeles, USA. Mice were housed and bred in aninstitutional specific pathogen free animal facility under standardconditions with a 12 hr light/dark cycle and fed a standard dietaccording to Animal Research Committee regulations at the University ofCalifornia, Los Angeles.

Doxycycline Treatment.

5 TG mice and 5 WT littermate control mice were maintained on normalwater until one month of age. After one month of age doxycycline wasadministered to the drinking water 2 g/L in 4% sucrose and kept inaluminum foil covered bottles to prevent light-induced degradation ofdoxycycline for a 3 week time period. The IL13 transgene exhibitsbaseline leakiness in the absence of doxycycline allowing transgenicmice to exhibit minor elevation of IL13 expression and minor allergicairway inflammation (Zheng 2000). For this reasoning non-treatedtransgenic mice were not used as controls in our experiments. After the3 week exposure to doxycycline all mice were euthanized and pathologicalassessments were conducted on the lungs.

Blood Collection.

Peripheral blood was collected by facial vein puncture using 5 mmsterile lancets (Medipoint Inc. Mineola, Ny) from experimental mice onspecified days throughout the duration of treatment and on sacrifice dayvia terminal right ventricle cardiac puncture using a heparin-coatedsyringe (American Pharmaceutical Partners, Inc. Schaumburg, Ill.). Bloodfrom each mouse was collected into EDTA-coated tubes (SarstedtAktiengesellschaft & Co., Numbrecht.

Immunofluorescence.

50 ul of whole peripheral blood was put into erythrocyte lysis buffer,cells were laid over poly-D-lysine-coated coverslips and fixed with 4%paraformaldehyde (Electron Microscopy Sciences) at room temperature asdescribed previously (Goldstine 2006). Subsequently, cells werepermeabilized with 0.5% Triton X-100 (Sigma), followed by 5 rinses inPBS. Blocking was done in aluminum-covered plates overnight at 4° C. in10% FBS. Coverslips were then incubated for 1 hour at room temperaturewith mouse anti-phospho-Histone H2A.X (Upstate, Temecula, Calif.) at adilution of 1:400, or Mouse anti-8-oxoguanine clone 483.15 (Upstate,Temecula, Calif.) at 1:250 respectively. Coverslips were then rinsedwith 0.1% Triton X-100. Following a second 10% FBS blocking, cells werestained with FITC-conjugated anti-mouse IgG (Jackson ImmunoResearch,West Grove, Pa.) at a dilution of 1:150 for samples with γH2AX primaryand (1:200) for samples with 8-oxoguanine primary, respectively for 1hour at room temperature. Coverslips were mounted onto slides usingVECTASHIELD with DAPI (Vector Laboratories, Burlingame, Calif.). Forboth 8-oxoguanine and γH2AX assay analysis were done on a Zeissautomated microscope. At least 100 cells were counted per sample andcells with more than four distinct foci in the nucleus were consideredpositive for γH2AX (Westbrook 2009) and cells that exhibited elevatedfluorescent intensity compared to background were considered positivefor 8-oxoguanine respectively. Apoptotic cells, which have anapproximate 10-fold increase in nuclear foci in damaged cells, were notincluded in analyses (Westbrook 2009; Muslimovic 2008). Statisticalanalyses were done using Poisson distribution 8-oxoguanine (STATAstatistical analysis software) for γH2AX and using ANOVA and Tukey'spost hoc test for 8-oxoguanine analysis (Graph Pad Prism).

Micronucleus Assay.

3 μl of whole blood were spread on a microscope slide and stained withWright-Giemsa solution (Sigma-Aldrich, St. Louis, Mo.). At least 4000erythrocytes were counted according to published recommendations(Hayashi 1994). MN were counted and scored with an Olympus Ax70 (Tokyo,Japan) at 100× magnification. Statistical analysis was done usingrepeated measures ANOVA followed by Tukey's post-tests (GraphPad Prism).

DNA Single Strand Breaks.

Oxidative DNA damage and DNA strand breaks were measured in peripheralblood cells using the alkaline comet assay. Peripheral blood wascollected before doxycycline administration (day 0), and on days 3, 6,9, 12, 15, 18 and 21 days of doxycycline treatment. Blood was diluted1:1 with RPMI+20% DMSO, slowly frozen and stored at −80° C. until theassay was performed. The comet assay was done as described previously(Singh 1988). Briefly, cells were mixed with low melting-point agarose,and placed in triplicate onto normal agarose layed over gelbond (LonzaInc. Rockland, Me.). The gel was immersed in lysis buffer (2.5 M NaCl,0.1 M EDTA, 10 mM Tris, 1% Triton, and 10% DMSO), then alkalineelectrophoresis buffer (0.3 M NaOH, 1 mM EDTA). After 20 minutes in theelectrophoresis buffer at 4° C., the gel was run for 45 minutes at 300mA, allowed to dry and then stained with SYBR Gold (Molecular Probes).Comet tail-moments were analyzed using CASP (Comet Assay SoftwareProject, http://casp.sourceforge.net/). To measure oxidative DNA damage,the comet assay was modified to include an incubation step with hOGG1(New England Biolabs, Ipswich, Mass.). As described previously, embeddedcells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37° C.for 30 minutes following the lysis step (Smith 2006). Tail-moments werenormalized to a control to account for inter-experimental variability.Statistical analyses were done using ANOVA (GraphPad Prism).

ELISA Analysis.

Serum was separated from blood by centrifugation on all mice immediatelybefore doxycycline administration (Day 0) and on days 3, 5, 7, 10, 13,16, 18, and 21. After collection serum samples were aliquoted intomicro-centrifuge tubes and kept at −20° C. until analysis. SandwichELISAs were conducted on samples that were diluted 1:10. Analysis oftotal Mouse IgE was done according to manufacturer's instructions (BDbiosciences). Each sample was done in triplicate and analyzed using therelative standard curve method optical density vs. concentration.Statistical analysis was done using linear mixed model with repeatedmeasurements nested within each mouse. (STATA statistical analysissoftware)

Gene Expression Analysis.

Lungs from WT and IL-13 mice at the end of the 3-week doxycyclineexposure mice were perfused and lavaged before immersion into RNAlater(Qiagen). Lungs were kept at 4° C. for 24 hours then transferred to −80°C. until RNA was isolated using the RNeasy Mini kit according tomanufacturer's instructions (Qiagen). cDNA was synthesized usingSuperscriptIII (Invitrogen) according to manufacturer's recommendations.Quantitative real-time PCR was performed on an ABI Prism 7500 geneexpression system (Applied Biosystems) using Taqman gene expressionassays for H2AX, 8-oxoguanine, IL-13, IL-4, IL-5, CCL-11/Eotaxin, TGF-β,Tnfα, and Gapdh was used as an internal control. Each reaction was donein triplicate and analyzed using the relative standard curve method.

Bronchoalveolar Lavage (BAL).

The amount of lung inflammation caused by increased infiltration ofimmune-circulating cells was assessed by BAL. Briefly, mice wereeuthanized the trachea was isolated via blunt dissection and smallcaliber tubing was inserted and secured in the airway. A volume of 1 mlof 1×PBS was flushed and removed 3 times successively from the lungs ofWT and IL-13 mice until 3 mL of BAL fluid was collected. BAL fluid wascentrifuged at 1600 rpm at 4° C. for 10 minutes. After centrifugationcells were re-suspended in 200 ul of 1×PBS. A 1:1 ratio of cells totrypan blue was put into a hemocytometer and the number of viable cellswas counted. After cell viability was assessed 200 ul of remaining cellswere put into cytospin and spun at 400 RPM for 5 minutes. Slides wereremoved from cytospin and allowed to air dry. After drying the slideswere stained using (Thermo Kwik Diff staining kit) using manufacturesstaining recommendation. Slides were allowed to air dry overnight andwere mounted with paramount and a coverslip and allowed to dry. Finallyat least 200 cells were differentiated by light microscopy based onconventional morphological criteria for each animal.

Immunohistochemistry.

γH2A.X, 8-Hydroxyguanosine, and Nitrotyrosine stains were done on lungtissue of (WT) and IL-13 mice. The slides were placed in xylene toremove paraffin, then a series of ethanol washes. After a wash in tapwater, the slides were incubated in 3% Hydrogen peroxide/methanolsolution for 10 minutes. The slides were then washed in distilled water,and incubated for 25 minutes in Citrate Buffer pH6 (InvitrogenCorporation) at 95 degrees Celsius using a vegetable steamer. Next, theslides were brought to room temperature, rinsed with PBST (PhosphateBuffered Saline containing 0.05% Tween-20), then incubated at roomtemperature for 1 hour with Anti-gamma H2A.X (phosphor S139) antibody(abcam, ab22551), 2 hours with anti-8-Hydroxyguanosine antibody (abcam,ab48508), or for 45 minutes with Nitrotyrosine (Millipore, 06-284) atthe dilutions of 1:50 for γH2A.X, and 8-Hydroxyguanosine antibodies andat 1:200 for the Nitrotyrosine antibody, respectively. The slides werethen rinsed with PBST, and were incubated with Dako EnVision+ System—HRPLabelled Polymer Anti-Mouse (Dako, K4001) at room temperature for 30minutes. Subsequently after a rinse with PBST, the slides were incubatedwith DAB (3,3′-Diaminobenzidine) for visualization. Finally, the slideswere washed in tap water, counterstained with Harris' Hematoxylin,dehydrated in ethanol, and mounted with media.

Results

Serum IgE Levels are Induced in IL-13 Mice.

Increased level of IgE is a major factor in the etiology of asthma andis found abundantly in the serum of both human and murine models ofasthma (Hamelmann 1999; Mora 2009; Wang 2009). Therefore we assessed thelevels of IgE in our transgenic IL-13 over-expression model. We observedthat the levels of IgE were higher in the transgenic mice 12 days afterIL-13 over-expression and were consistently higher throughout theexperiment until terminal day 21 (FIG. 21). Although IL-13 miceexhibited higher IgE levels this induction was only significant at day21 at **, p<0.007

IL-13 Mice Exhibit Increased Inflammation of the Lung.

To understand the role IL-13 induced lung inflammation plays in thegenotoxicity and progression of asthma we compared the lungs of WT andIL-13 animals. In (FIGS. 22A and 22C) WT animals exhibit no increase ofinflammation.

In contrast IL-13 mice (FIGS. 22B and 22D) exhibit significantinflammation of the lung characterized in the airways bronchiolar lumen.IL-13 mice showed increased inflammatory cells migration in thebronchiolar epithelium, marked hyperplasia, goblet cell metaplasia, andeosinophilic intracytoplasmic inclusion bodies present in clara cells.Thus IL-13 increases inflammation via recruitment of inflammatory cellsmigrating into airway spaces.

IL-13 Mice Exhibit Increased Immune Cell Infiltration in BAL Fluid.

To delineate what immune cells may be implicated in the persistentinflammatory and genotoxic response present in the asthma mouse model wedetermined the cellular composition of the BAL fluid in both the WT andIL-13 mice. IL-13 animals had a near 5-fold increase in eosinophilpresence in BAL fluid compared to WT animals at p<0.04 (FIG. 23). IL-13mice also exhibited significantly more circulation of neutrophils in theBAL fluid at ***, p<0.0004 compared to WT littermates. IL-13 mice alsoexhibited an increase induction of lymphocytes although this observationwas not significantly different from WT animals.

IL-13 Mice Exhibit Persistent Inflammation Induced Immune Response.

To elucidate the role IL-13 plays in up-regulation of inflammation inthe lung we assessed key mediators of asthma FIGS. 24A-24C, inflammatorydisease FIGS. 24D-24F, and genotoxicity FIG. 24G via quantitativereal-time PCR. As a measurement of further efficacy of our tissuespecific asthma model we measured IL-13 levels in the lungs of bothgroups of experimental mice. The asthma mouse model exhibited anexpected significant increased gene expression of IL-13 at **, p<0.001compared to WT animals. IL-4, TNF-α, IL-5 were significantlyup-regulated in IL-13 mice at *, p<0.01 compared to WT animals. IL-13mice also displayed a marked increase of TGF-β FIG. 21-6E at **, p<0.001compared to WT mice. Coil transcript levels in IL-13 mice were slightlyhigher but did not show a significant increase compared to WT mice FIG.21-6G These data are indicative of a chronically activated innate immuneresponse present in IL-13 mice compared to WT mice.

IL-13 Mice have Increased Staining of Markers of Genotoxicity in LungTissue.

To further assess asthma induced genotoxicity, the lungs of WT and IL-13mice were stained with γH2AX, anti-8-Hydroxyguanosine, and Nitrotyrosineantibodies. IL-13 mice exhibited increased staining with markers ofgenotoxicity in the lungs in comparison to WT animals (FIG. 25).

IL-13 Mice Show Systemically Elevated Reactive Oxygen Species InducedGenotoxicity and Double Stranded Breaks in Peripheral Blood.

Because IL-13 is a major mediator of allergenic asthma and induceshigher levels of inflammation in asthmatic mice (Elias 2003), wehypothesized that inflammation induced systemic DNA damage would be moreprevalent in IL-13 compared to wild type (WT) mice. Increase of asthmainduced genotoxicity was assessed in peripheral white blood cells as asystemic measurement of DNA damage. 8-oxoguanine is a mutagenic lesioncaused by the interaction of a reactive oxygen species to DNA thatcauses G:C to T:A transversion mutations during replication (Westbrook2010). Percent positive 8-oxoguanine staining in peripheral white bloodcells was assessed using fluorescent microscopy. Blood was taken on day0 as an assessment of baseline levels of 8-oxoguanine induction betweenboth WT and IL-13 groups. After 6 days of doxycycline presence indrinking water IL-13 mice exhibited a slight increase of 8-oxoguanineimmuno-staining compared to wild type mice this induction persisted andbecame statistically significant at **, p<0.001 at day 15 and remainedelevated throughout the 21 day exposure to doxycycline (FIG. 26A). As ameasure of the amount of genotoxicity caused by an accumulation of DNAdouble strand breaks the γH2AX assay was assessed in the WT and IL-13animals. H2AX is a member of the histone H2A protein family and becomesrapidly phosphorylated in presence of a DNA damaging event (Bonner2008). This rapid phosphorylation causes recruitment of DNA repairproteins to the site of the break and is detectable by specificantibodies to γH2AX. In FIG. 26B we assessed the amount of double strandbreaks present in the WT and IL-13 animals. Transgenic animals exhibitedan increase in the amount of double strand breaks occurring at everytime point after over-expression. This induction of γH2AX wassignificant on day 9 at **, p<0.002, at day 12 at *, p<0.02, and at day18 day at **, p<0.001 respectively. A nearly significant induction ofγH2AX at P=0.064 on day 21 was also observed in the IL-13 mice.

IL-13 Mice have Systemic Single Strand Breaks and Persistent SystemicGenotoxicity that Induces Comet and Micronucleus Formation in PeripheralBlood Leukocytes Respectively.

The in vivo micronucleus assay was conducted in mature normochromaticerythrocytes circulating in the peripheral blood to determinechromosomal damage. Micronuclei in erythrocytes/erythroblasts from theperipheral blood or bone marrow have been induced in the presence ofchromosome breaks, spindle abnormalities, or structurally abnormalchromosomes (Hayashi 1994, Westbrook 2010). Mature micronucleatednormochromatic erythrocytes represent the final developmental stage oferythroblasts containing micronuclei stemming in the bone marrow, andpermit the simultaneous study of the generation and elimination ofmicronucleated erythrocytes (Steinheider 1986, Westbrook 2010). Bloodwas taken on day 0 as an assessment of baseline levels of 8-oxoguanineinduction between both WT and IL-13 groups. After 6 days of doxycyclinepresence in drinking water IL-13 mice exhibited a significant increaseof micronuclei formation in peripheral blood compared to WT animals at*, p<0.05. This statistically significant induction at *, p<0.05 ofmicronuclei persisted until terminal date Day 21. (FIG. 27A)

The alkaline comet assay is a gel electrophoresis assay that allows thedetection of single and double strand breaks, and alkali labile sites atthe single cell level (Westbrook 2009). Asthma is an inflammatorydisease that produces large amounts of reactive oxygen species (ROS)(Hasbal; Luzina). Interaction of ROS with DNA may result in mutagenicoxidative base modifications such as 8-hydroxydeoxyguanosine(8-oxo-dGuo) and induce DNA strand breaks (Hasbal). Transgenic animalsexhibited an increase in the amount of single strand breaks occurringafter 6 days of IL-13 over-expression compared to all other groups whereno increase was observed. This induction of strand breaks wassignificant for indicated groups at *, p<0.05. (FIG. 27B)

Discussion

Asthma is a chronic obstructive lung disease characterized by chronicinflammation of the airways and recurrent bronchospasms ranging frommild to debilitating (Bosse 2009). It is well established thatInterleukin-13 serves as a major mediator of the asthmatic process(Wills-Karp 1998). This study is the first to assess IL-13 role ingenotoxicity concomitantly with the inflammatory asthmatic process. Ourstudy also demonstrates for the first time that this genotoxicityextends beyond the primary site of the lung to circulating leukocytesand erythroblasts in the bone marrow eliciting systemic effect inperipheral blood driven by IL-13 overexpression in the lungs.

IL-13 mice exhibited an asthmatic phenotype consistent with previousdata. We found a significant increase in IgE. IL-13 mice hadsub-epithelial eosinophilic infiltration, peribronchiolar, andperivascular lymphoid infiltration, free floating eosinophilic crystals,many surrounded by aggregates of macrophages, giant cells and neutrophilPMNs (Wills-Karp 1998; Fireman 2003; Grunig 1998). IL-13 mice showed asignificant influx of eosinophils, a cellular hallmark of asthma (Conroy1997), a significant increase in neutrophils, and non-significantincrease of lymphocytes in the bronchoalveolar lavage fluid. Transgenicmice had increased gene expression of IL-13, IL-4, IL-5, TNFα, Tgfβ,γH2AX, and Ccl11 produced in the lungs (Ma 2006; Elias2003; Wynn 2003;Vanoirbeek 2009). There was a significant increase in γH2AX levels inthe lungs of the IL-13 mice and an induced yet non-significant increasein 8-oxoguanine. In IL-13 mice, we detected a significant increase ofsingle and double stranded breaks in the peripheral blood and lung, asignificant induction of micronucleus formation in the normochromaticerythrocytes present in the peripheral blood leukocytes, as well asincreased staining of markers of genotoxicity in the lung (Westbrook2010).

We utilized the well characterized inducible over-expressionCC10-rtTA-IL13 transgenic (TG) mouse to elucidate the effectinterleukin-13 may have in the genotoxicity of asthma. Recent work hasshown that IL-13 signaling is mediated by the type-2 IL-4 receptor,which consists of the IL-4R alpha and IL-13R alpha 1 chains (Munitz2008; Mentink-Kane 2004), yet IL-13 alone is necessary and sufficient torender the major pathophysiological effects of asthma (Wills-Karp 1998).IL-4 along with IL-13 is a key mediator of inflammation, has anoverlapping biological function as IL-13, yet has a distinct role inasthma progression (Munitz 2008). IL-4 is best known for its role fordefining the Th2 phenotype of lymphocytes in asthma, but alsoexacerbating the asthmatic phenotype by increasing airwayhyperresponsiveness, eosinophil recruitment, and mucus over-production(Wills-Karp 1998; Grunig 1998). We next investigated mRNA levels ofCCL-11/eotaxin. There was not a significant increase in CCL-11/eotaxintranscript present in the lung mRNA, however, we did observe asignificant increase in IL-5 lung mRNA transcript. A possibleexplanation to the induced yet non-significant increase in CCL11/eotaxintranscript may be found in the work of (Humbles 1997). These datasuggest, in corroboration with (Conroy 1997), that migrating eosinophilsin the bronchoalveolar lavage fluid may stimulate release of IL-5, butnot CCL11/eotaxin.

With regards to the genotoxicity of IL-13 induced asthma we discoveredan increase in the amount of γH2AX and 8-oxoguanine in the blood andlungs of these mice. Phosphorylation of histone H2A to form γH2AX in thepresence of a DNA damaging event is used as a biomarker of cellularresponse to DSBs and has a potential for monitoring DNA damage andrepair in human and mice (Valdiglesias 2013; Yamamoto 2008).8-oxo-7,8-dihydroguanine (8oxoG) is an abundant ROS induced lesion thatwhen accumulated has been associated with numerous diseases, includingcancer (Westbrook 2009; Evans 2004; Fortini 2003). We did observe aslight increase of 8oxoG in the WT animals which most likely can beattributed to the repeated blood draws that caused a moderate increasein the production of stress related ROS-induced DNA damage similarlyfound in (Westbrook 2010). As a measure of ongoing DNA damage Westbrook,et. al (Westbrook 2010) show that an accumulation of double-strandbreaks can lead to chromosome breaks and micronucleus formation.Perturbations to erythroblasts in the bone marrow may be a humoraleffect of inflammation-associated DNA damage, as with the peripheralleukocytes. We suggest that increased inflammation in our experimentalmice causes a significant induction of migratory cells thatpreferentially release pro-inflammatory cytokines at sites ofinflammation. This re-circulating pool of activated cells may recruitmore effector cells, which come into contact with erythroblasts in thebone marrow causing the observed clastogenicity.

To evaluate the inflammatory cell composition we determined thedifferential cell percentages. The increased prevalence of neutrophilsover that of eosinophils in the bronchoalveolar lavage fluid may depictthe presence of a more chronic asthmatic phenotype, an idea supported by(Kamath 2005). Moreover this significant influx of both neutrophils andeosinophils may help generate the enhanced systemic genotoxic responsefound in the blood. This observation of an induction of γH2AX mRNAlevels further confirms increased genotoxicity in IL-13 mice andcorrelates with our hypothesis of systemic genotoxicity.

In conclusion, we proposed that the key asthmatic mediatorinterleukin-13, increases important elements of the inflammatoryresponse including ROS derived oxidative stress causing an induction ingenotoxicity that has wide reaching systemic genotoxic effects, such asoxidative DNA damage, single and double DNA strand breaks, micronucleusformation, and protein nitration in the peripheral blood. Two potentialexplanations for the local inflammation and systemic genotoxicity aredescribed by Westbrook et al (Westbrook 2010). In the first model,innate immune cells activated by inflammation release reactive speciesthat damage circulating leukocytes in the periphery. In the secondmodel, inflammatory cytokines are responsible for systemic genotoxicitythrough cytokine receptor mediated production of free radicals thatdamage distant leukocytes. These models are not mutually exclusive.Making the second model more likely, it has been shown that injection ofcytokines causes systemic genotoxicity in mice (Westbrook 2010). Wefurther suggest increased immune cell infiltration and inflammationbyproducts as a possible culprit to this genotoxic induction. Theinduction of systemic strand breaks which are prevalent in many types ofcancer were found to be significantly increased in our IL-13 inducedasthma model. Recent studies also point to the fact that asthmaticpatients have higher cancer risk (Boffetta 2002; Brown 2006; Garcia Sanz2011). Previous studies in human asthmatics also identified increasedstrand breaks produced during the direct interaction of ROS with DNA orduring the repair process of damaged DNA (Hasbal; Zeyrek 2009). Insummary, asthma is associated with systemic genotoxicity through singleand double DNA strand breaks, oxidative DNA damage, protein nitration,and micronucleus formation. This study further implicates IL-13 as apotential therapeutic target for other pulmonary diseases involvingcarcinogenesis. In addition, systemic genotoxicity might be a convenientblood marker for the extent and severity of asthma.

REFERENCES CITED IN EXAMPLE 5

-   Akdis, M., et al., J Allergy Clin Immunol, 2011. 127(3): p.    701-21e1-70.-   Akinbami, L. J., et al., Natl Health Stat Report, 2011(32): p. 1-14.-   Boffetta, P., et al., Eur Respir J, 2002. 19(1): p. 127-33.-   Brown, D. W., et al., Cancer Causes Control, 2006. 17(3): p. 349-50.-   Bradley, B. L., et al., J Allergy Clin Immunol, 1991. 88(4): p.    661-74.-   Bonner, W. M., et al., Nat Rev Cancer, 2008. 8(12): p. 957-67.-   Bosse, Y., et al., Respir Res, 2009. 10: p. 98.-   Chatila, T. A., Trends Mol Med, 2004. 10(10): p. 493-9.-   Cohn, L., et al., Annu Rev Immunol, 2004. 22: p. 789-815.-   Conroy, D. M., et al., Mem Inst Oswaldo Cruz, 1997. 92 Suppl 2: p.    183-91.-   Elias, J. A., et al., Chest, 2003. 123(3 Suppl): p. 339S-45S-   Evans, M. D., et al., Mutat Res, 2004. 567(1): p. 1-61.-   Fireman, P., Allergy Asthma Proc, 2003. 24(2): p. 79-83.-   Fortini, P., et al., Mutat Res, 2003. 531(1-2): p. 127-39.-   Garcia Sanz, M. T., et al., Clin Transl Oncol, 2011. 13(10): p.    728-30.-   Goldstine, J. V., et al., DNA Repair (Amst), 2006. 5(4): p. 432-43.-   Grunig, G., et al., Science, 1998. 282(5397): p. 2261-3.-   Hamelmann, E., et al., Allergy, 1999. 54(4): p. 297-305.-   Hasbal, C., et al., Pediatr Allergy Immunol. 21(4 Pt 2): p. e674-8.-   Harrington, L. E., et al., Nat Immunol, 2005. 6(11): p. 1123-32.-   Hayashi, M., et al., Mutat Res, 1994. 312(3): p. 293-304.-   Henderson, W. R., Jr., et al., J Exp Med, 1996. 184(4): p. 1483-94.-   Humbles, A. A., et al., J Exp Med, 1997. 186(4): p. 601-12.-   Hyde, D., et al., European Respiratory Review, 2006. 15(101): p.    122-135.-   Jiang, H., et al., J Allergy Clin Immunol, 2000. 105(6 Pt 1): p.    1063-70.-   Kamath, A., et al., Thorax, 2005. 60(7): p. 529-30.-   Luzina, I. G., et al., J Leukoc Biol. 92(4): p. 753-64.-   Ma, B., et al., J Immunol, 2006. 176(8): p. 4968-78.-   Mattes, J., et al., J Exp Med, 2002. 195(11): p. 1433-44.-   Medoff, B. D., et al., Annu Rev Immunol, 2008. 26: p. 205-32.-   Mentink-Kane, M. M. and T. A. Wynn, Immunol Rev, 2004. 202: p.    191-202.-   Miller, A. L., Alternative medicine review: a journal of clinical    therapeutic, 2001. 6(1): p. 20.-   Mora, J., et al., Clin Immunol, 2009. 132(1): p. 132-40.-   Munitz, A., et al., Proc Natl Acad Sci USA, 2008. 105(20): p.    7240-5.-   Muslimovic, A., et al., Nat Protoc, 2008. 3(7): p. 1187-93.-   Ooi, A. T., et al., Am J Transl Res, 2012. 4(2): p. 219-28.-   Romanet-Manent, S., et al., Allergy, 2002. 57(7): p. 607-13.-   Singh, N. P., et al., Exp Cell Res, 1988. 175(1): p. 184-91.-   Smith, C. C., et al., Mutagenesis, 2006. 21(3): p. 185-90.-   Steinheider, G., et al., Cell Biol Toxicol, 1986. 2(1): p. 197-211.-   Valdiglesias, V., et al., Mutat Res, 2013.-   Vanoirbeek, J. A., et al., Scand J Immunol, 2009. 70(1): p. 25-33.-   Wang, X. H., et al., Zhonghua Jie He He Hu Xi Za Zhi, 2009.    32(3): p. 161-4.-   Westbrook, A. M., et al., Cancer Res, 2009. 69(11): p. 4827-34.-   Westbrook, A. M., et al., Cancer Res, 2009. 69(11): p. 4827-34.-   Westbrook, A. M. and R. H. Schiestl, 2010 Cancer Res. 70(5): p.    1875-84.-   Wills-Karp, M., et al., Science, 1998. 282(5397): p. 2258-61.-   Wynn, T. A., Annu Rev Immunol, 2003. 21: p. 425-56.-   Yamamoto, M. L., et al., Mutat Res, 2008. 644(1-2): p. 11-6.-   Zeyrek, D., et al., Pediatr Allergy Immunol, 2009. 20(4): p. 370-6.-   Zheng, T., et al., J Clin Invest, 2000. 106(9): p. 1081-93.-   Zimmermann, N., et al., J Clin Invest, 2003. 111(12): p. 1863-74.

Throughout this application various publications are referenced. Thedisclosures of these publications in their entireties are herebyincorporated by reference into this application in order to describemore fully the state of the art to which this invention pertains.

From the foregoing it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention. Accordingly, the invention is notlimited except as by the appended claims.

What is claimed is:
 1. A method for detection and treatment of allergicinflammation, the method comprising: (a) contacting a test sample ofperipheral leukocytes from a subject with reagents for assaying for amarker of DNA damage; (b) measuring the amount of marker present in thetest sample as compared to a control sample; and (c) treating thesubject for allergic inflammation if the measured amount of marker inthe test sample is increased as compared to the control sample, whereinthe treating for allergic inflammation comprises a treatment thattargets IL-13.
 2. The method of claim 1, wherein the marker of DNAdamage is single- and/or double-stranded breaks in leukocytes.
 3. Themethod of claim 2, wherein the measuring comprises an immunoassay forγ-H2AX and/or an alkaline comet assay.
 4. The method of claim 1, whereinthe marker of DNA damage is oxidative DNA damage in leukocytes.
 5. Themethod of claim 4, wherein the measuring comprises an enzymehOgg1-modified comet assay or an immunoassay for 8-oxoguanine.
 6. Themethod of claim 1, wherein the peripheral leukocyte is a lymphocyte or amonocyte.
 7. The method of claim 1, wherein the sample of peripheralleukocytes is obtained from peripheral blood, or fluid of a body cavity.8. The method of claim 7, wherein the fluid of a body cavity is pleural,peritoneal, cerebrospinal, mediastinal, or synovial fluid.
 9. The methodof claim 1, wherein the allergic inflammation is allergic asthma.
 10. Amethod for treating allergic inflammation in a subject, the methodcomprising: (a) contacting a test sample of peripheral blood leukocytesobtained from a subject at a first time point with reagents for assayingfor a marker of DNA damage; (b) contacting a test sample of peripheralleukocytes obtained from the subject at a second time point withreagents for assaying for a marker of DNA damage, wherein the subjecthas been treated for inflammatory disease prior to the second timepoint; (c) measuring the amount of marker present in the test samplesobtained at the first and second time points; (d) determining whether adecreased amount of marker is present in the test sample obtained at thesecond time point compared to the test sample obtained at the first timepoint, which decreased amount of marker is indicative of reduced DNAdamage; and (e) modifying the treatment for inflammatory disease if adecreased amount of marker is not present at the second time pointcompared to the first time point, wherein the treatment for allergicinflammation comprises a treatment that targets IL-13.
 11. The method ofclaim 10, wherein the marker of DNA damage is single- and/ordouble-stranded breaks in leukocytes.
 12. The method of claim 11,wherein the measuring comprises an immunoassay for γ-H2AX and/or analkaline comet assay.
 13. The method of claim 10, wherein the marker ofDNA damage is oxidative DNA damage in leukocytes.
 14. The method ofclaim 13, wherein the measuring comprises an enzyme hOgg1-modified cometassay or an immunoassay for 8-oxoguanine.
 15. The method of claim 10,wherein the allergic inflammation is allergic asthma.
 16. The method ofclaim 1, wherein the increase in measured amount of marker in the testsample as compared to the control sample is a statistically significantincrease.
 17. The method of claim 10, wherein the modifying comprisesincreasing the treatment dose or changing to a different therapeuticagent.